Contacts of the helix formed by residues 87 - 109 (chain A) in PDB entry 5KAL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ALA* 3.6 9.7 - - + +
86A ALA* 1.3 85.8 - - - +
88A GLN* 1.3 63.9 + - - +
89A VAL* 3.8 12.0 + - - +
90A ALA* 3.4 21.5 + - - +
91A LYS* 3.4 21.7 + - - +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 4.1 0.2 + - - -
87A THR* 1.3 72.4 - - - +
89A VAL* 1.3 69.0 + - + +
91A LYS* 3.2 36.9 + - - +
92A GLY* 2.9 19.1 + - - -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 3.3 10.0 - - - +
88A GLN* 1.3 78.4 - - + +
90A ALA* 1.3 62.4 + - - +
92A GLY* 3.0 11.6 + - - -
93A LEU* 3.0 37.3 + - + +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 4.4 24.0 - - + +
87A THR* 3.4 19.6 + - - +
88A GLN 3.3 0.4 - - - -
89A VAL* 1.3 79.7 - - - +
91A LYS* 1.3 63.7 + - + +
92A GLY 3.2 0.2 + - - -
93A LEU* 3.3 12.0 + - - +
94A GLN* 3.0 39.7 + - - +
141A ARG* 5.7 0.7 - - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 4.8 9.6 - - - +
87A THR 3.4 13.4 + - - +
88A GLN* 3.2 41.8 + - - +
90A ALA* 1.3 77.1 - - + +
92A GLY* 1.3 57.0 + - - +
94A GLN* 3.9 8.7 - - - +
95A ALA* 2.9 30.5 + - - +
120A THR 4.1 17.0 + - - +
121A ARG* 3.7 23.7 + - - +
123A PRO* 4.2 19.6 - - + +
141A ARG* 4.4 9.4 - - - +
285A ASN* 5.8 3.6 - - - +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLN 2.9 13.5 + - - -
89A VAL* 3.0 5.3 + - - -
91A LYS* 1.3 74.3 - - - +
93A LEU* 1.3 67.0 + - - +
95A ALA* 3.2 6.4 + - - +
96A ASP* 2.9 24.0 + - - +
209B PRO* 6.4 2.5 - - - -
264B PRO* 5.2 1.4 - - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.0 44.9 + - + +
90A ALA* 3.3 8.7 + - - +
92A GLY* 1.3 74.3 - - - +
94A GLN* 1.3 64.5 + - - +
96A ASP* 3.1 8.3 + - + +
97A ILE* 3.0 24.9 + - - +
140A TYR* 4.3 18.5 - - + -
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA 5.5 0.4 + - - -
90A ALA* 3.0 30.4 + - - +
91A LYS* 3.9 4.8 - - - +
93A LEU* 1.3 75.4 - - - +
95A ALA* 1.3 64.8 + - - +
97A ILE* 3.2 8.9 - - - +
98A LEU* 3.0 35.8 + - + +
123A PRO* 3.5 23.3 - - + +
139A ALA* 3.3 26.3 + - + +
140A TYR* 3.8 20.2 + - + +
141A ARG* 3.2 47.6 + - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS 2.9 19.8 + - - +
92A GLY* 3.7 5.8 - - - +
94A GLN* 1.3 76.4 - - - +
96A ASP* 1.3 58.0 + - - +
98A LEU* 3.8 5.1 - - - +
99A ALA* 2.9 29.8 + - - +
116A GLU* 5.2 0.7 - - - +
118A ARG* 6.2 4.3 - - + -
123A PRO* 4.7 12.7 - - + +
264B PRO* 4.1 18.3 - - + +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 2.9 16.6 + - - +
93A LEU* 3.6 7.9 - - + +
95A ALA* 1.3 76.9 - - - +
97A ILE* 1.3 62.5 + - - +
99A ALA* 3.1 13.7 + - - +
100A LYS* 3.1 35.8 + - - +
206B GLN* 4.8 6.2 + - - -
207B PHE* 4.1 22.1 + - + +
264B PRO* 3.8 22.6 - - + +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.0 25.4 - - + -
44A ASP* 6.0 0.2 - - + -
47A MET* 4.1 21.5 - - + -
71A VAL* 6.0 0.9 - - + -
93A LEU 3.0 14.4 + - - +
94A GLN 3.2 11.9 - - - +
96A ASP* 1.3 76.9 - - - +
98A LEU* 1.3 67.4 + - + +
100A LYS* 3.2 15.8 + - + +
101A LEU* 3.0 24.3 + - + +
139A ALA* 3.9 17.3 - - + -
140A TYR* 3.8 33.9 - - + +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 5.9 0.9 - - + -
94A GLN* 3.0 23.8 + - + +
95A ALA* 3.9 4.0 - - - +
97A ILE* 1.3 79.5 - - + +
99A ALA* 1.3 57.7 + - - +
101A LEU* 3.8 10.5 - - + +
102A ALA* 2.9 31.4 + - - +
116A GLU* 5.0 0.9 - - + -
123A PRO* 3.8 38.6 - - + +
124A VAL* 4.0 8.3 - - - +
125A VAL* 3.7 20.8 - - + +
137A ILE* 4.0 24.9 - - + +
138A THR* 4.1 20.0 - - - +
139A ALA* 4.1 11.9 - - + +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA 2.9 14.7 + - - +
96A ASP* 3.1 10.5 + - - +
98A LEU* 1.3 74.3 - - - +
100A LYS* 1.3 65.0 + - + +
102A ALA* 3.3 3.3 + - - +
103A ARG* 3.0 29.7 + - - +
106A ARG* 5.0 0.9 + - - -
116A GLU* 3.8 16.5 + - - +
264B PRO* 4.1 7.4 - - + +
265B GLY* 3.8 33.7 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.4 19.1 - - + -
96A ASP* 3.1 29.5 + - - +
97A ILE* 3.2 19.1 + - + +
99A ALA* 1.3 76.9 - - + +
101A LEU* 1.3 64.0 + - - +
103A ARG* 3.0 32.1 + - - +
104A VAL* 3.0 16.7 + - + +
203B ASN* 3.7 27.8 + - - +
206B GLN* 3.5 25.8 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 6.3 0.2 - - + -
39A CYS* 4.0 11.4 - - + -
40A VAL* 3.9 31.2 - - + +
43A VAL* 3.8 27.2 - - + +
47A MET* 6.1 2.9 - - + -
71A VAL* 4.4 15.0 - - + -
97A ILE* 3.0 18.6 + - + +
98A LEU* 3.8 12.6 - - + +
100A LYS* 1.3 75.3 - - - +
102A ALA* 1.3 64.1 + - - +
104A VAL* 3.1 4.7 + - + +
105A ILE* 2.9 35.0 + - + +
125A VAL* 6.2 1.8 - - + -
137A ILE* 4.1 33.7 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 2.9 19.0 + - - +
99A ALA 3.3 4.2 + - - +
101A LEU* 1.3 75.3 - - - +
103A ARG* 1.3 64.7 + - - +
105A ILE* 3.2 8.5 + - - +
106A ARG* 2.9 30.7 + - - +
114A VAL* 3.9 24.6 - - + +
116A GLU* 4.1 24.9 - - + +
125A VAL* 4.3 6.7 - - + +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.0 15.3 + - - +
100A LYS* 3.1 28.7 - - - +
102A ALA* 1.3 77.6 - - - +
104A VAL* 1.3 65.8 + - + +
106A ARG* 3.2 17.1 + - - +
107A GLN* 3.0 21.3 + - + +
200B LEU 4.1 10.9 + - - -
201B GLN* 3.3 46.9 + - - +
203B ASN* 3.1 37.7 + - - +
265B GLY* 5.1 12.1 - - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 4.2 15.9 - - + +
42A ALA* 3.7 30.5 - - + +
43A VAL* 3.8 20.2 - - + +
100A LYS* 3.0 12.3 + - + +
101A LEU 3.6 5.8 - - - +
103A ARG* 1.3 78.3 - - + +
105A ILE* 1.3 64.5 + - - +
107A GLN* 2.9 26.5 + - - +
108A LYS* 3.0 24.8 + - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 6.0 2.2 - - + -
39A CYS* 4.0 28.0 - - + -
101A LEU* 2.9 36.9 + - + +
102A ALA* 3.6 11.0 - - - +
104A VAL* 1.3 75.3 - - - +
106A ARG* 1.3 63.5 + - - +
108A LYS* 3.1 2.8 + - - +
109A HIS* 3.0 25.0 + - + +
112A TRP* 4.1 25.1 - - + -
114A VAL* 3.6 23.1 - - + -
125A VAL* 5.2 2.5 - - + -
127A VAL* 4.6 11.9 - - + -
135A PHE* 5.2 2.7 - - + -
137A ILE* 4.0 22.4 - - + -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 5.0 1.2 + - - -
102A ALA* 2.9 23.3 + - - +
103A ARG* 3.7 17.9 - - - +
105A ILE* 1.3 76.0 - - - +
107A GLN* 1.3 63.0 + - - +
109A HIS 3.2 20.8 - - - +
110A LEU* 4.2 9.2 + - - +
112A TRP 5.5 2.9 - - - +
114A VAL* 3.2 49.5 + - + +
116A GLU* 3.1 28.9 + - - +
265B GLY* 5.6 0.6 - - - -
266B ILE* 3.3 34.0 - - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.0 13.1 + - + +
104A VAL* 2.9 24.0 + - - +
106A ARG* 1.3 80.4 - - - +
108A LYS* 1.3 65.7 + - + +
109A HIS 3.7 0.7 + - - -
110A LEU* 5.3 1.0 + - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 4.8 19.2 + - + +
39A CYS* 4.4 17.9 - - - +
42A ALA* 4.6 18.5 - - - +
104A VAL* 3.0 21.2 + - + +
105A ILE 3.1 0.4 + - - +
107A GLN* 1.3 85.4 - - + +
109A HIS* 1.3 81.3 + - + +
110A LEU 4.2 0.4 - - - -
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.7 21.0 + - + +
39A CYS* 4.8 11.9 - - - -
105A ILE* 3.0 12.9 + - + +
106A ARG* 3.2 16.2 - - - +
108A LYS* 1.3 97.1 + - + +
110A LEU* 1.3 63.3 + - - +
111A SER* 3.5 0.9 - - - +
112A TRP* 3.4 80.3 + + + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il