Contacts of the helix formed by residues 86 - 103 (chain A) in PDB entry 1KEK
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 ALA 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.5 17.2 - - + +
31A THR 4.4 1.6 - - - +
32A PRO* 4.2 6.5 - - + -
33A SER* 4.5 0.9 - - - -
85A THR* 1.3 81.3 + - - +
87A SER* 1.3 64.1 + - - +
88A GLN 3.3 0.3 + - - -
89A GLY* 2.8 29.3 + - - -
90A LEU* 3.1 5.7 + - - -
111A VAL* 4.2 5.2 - - - -
112A THR* 3.1 32.5 - - - +
114A ARG* 4.2 5.8 - - + -
129A ASP* 3.8 2.0 - - - -
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Residues in contact with SER 87 (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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30A ILE* 4.4 0.9 - - - -
86A ALA* 1.3 70.5 - - - +
88A GLN* 1.3 82.8 + - - +
90A LEU* 2.9 14.0 + - - +
91A LEU* 3.3 12.6 + - - +
114A ARG* 3.2 40.9 + - - -
115A ALA 2.8 21.1 + - - -
116A ILE* 3.5 9.3 - - - +
129A ASP* 2.7 29.5 + - - +
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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
----------------------------------------------------------
30A ILE* 4.2 1.5 - - + +
87A SER* 1.3 92.2 + - - +
89A GLY* 1.3 62.4 + - - +
91A LEU* 3.5 23.0 + - - +
92A LEU* 3.3 26.7 + - - +
114A ARG* 4.5 8.9 + - - +
115A ALA 4.3 0.5 - - - +
116A ILE* 3.7 6.2 - - - +
117A ALA* 2.9 40.0 + - + +
121A LEU* 5.6 2.2 - - + -
868A LEU* 3.5 26.3 - - + +
869A PHE 6.3 0.2 - - - +
870A GLU* 5.1 3.0 + - - +
2236A HTL 3.4 38.5 - - + +
95B PRO* 4.4 7.3 + - - +
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Residues in contact with GLY 89 (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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30A ILE* 3.7 3.2 - - - +
64A GLU* 3.3 46.8 - - - +
85A THR* 3.5 8.1 - - - -
86A ALA 2.8 9.7 + - - -
88A GLN* 1.3 79.6 - - - +
90A LEU* 1.3 65.7 + - - +
92A LEU 3.1 9.7 + - - -
93A MET* 3.3 9.2 + - - +
2236A HTL 4.2 0.2 - - - -
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Residues in contact with LEU 90 (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 THR* 3.5 25.2 + - + -
86A ALA* 3.1 11.5 + - - -
87A SER 2.9 9.6 + - - +
89A GLY* 1.3 77.5 - - - +
91A LEU* 1.3 56.5 + - + +
93A MET* 2.9 20.7 + - + +
94A ILE* 3.2 11.8 + - + +
97A MET* 3.6 15.9 - - - -
109A PHE* 4.3 6.7 - - + -
111A VAL* 4.3 10.8 - - + -
129A ASP* 3.6 35.7 - - + +
130A ILE* 4.0 5.6 - - - +
133A ALA* 4.4 6.7 - - + -
168A MET* 3.2 38.8 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER 3.3 11.9 + - - +
88A GLN* 3.5 15.9 - - - +
89A GLY 3.2 0.6 - - - -
90A LEU* 1.3 74.8 - - + +
92A LEU* 1.3 63.3 + - - +
94A ILE* 3.2 32.1 + - + +
95A PRO* 4.0 3.6 - - - +
116A ILE* 3.8 28.3 - - + -
129A ASP* 4.9 3.8 - - - +
132A ALA* 3.7 29.4 - - + -
91B LEU 5.3 4.7 - - - +
94B ILE* 4.5 5.2 - - + +
95B PRO* 3.9 40.6 - - + +
98B TYR* 4.0 17.5 - - + -
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Residues in contact with LEU 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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63A SER* 4.4 4.5 - - - -
64A GLU* 3.9 9.9 - - + +
65A ALA* 3.6 41.3 - - + +
68A ALA* 5.0 0.3 - - - +
88A GLN 3.3 13.4 + - - +
89A GLY 3.1 8.9 + - - +
91A LEU* 1.3 76.1 - - - +
93A MET* 1.3 61.8 + - - +
94A ILE 3.3 0.2 - - - -
95A PRO* 3.7 10.8 - - - +
96A ASN* 5.5 0.3 + - - +
870A GLU* 3.7 25.4 - - + +
969A ILE* 4.3 12.1 - - + -
2236A HTL 3.6 23.1 - - + -
92B LEU* 6.0 4.4 - - + +
95B PRO* 4.1 15.3 - - + -
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Residues in contact with MET 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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28A TYR* 6.0 0.9 - - + +
64A GLU* 3.7 34.8 - - + +
67A ALA* 4.2 7.6 - - + -
68A ALA* 3.8 17.0 - - + -
83A THR* 3.8 26.7 - - + +
84A PHE 4.9 0.7 - - - +
85A THR* 3.7 32.1 - - - -
89A GLY 3.4 11.2 - - - +
90A LEU* 2.9 10.2 + - - +
92A LEU* 1.3 78.5 - - - +
94A ILE* 1.3 64.9 + - - +
95A PRO* 3.3 2.5 - - - -
96A ASN* 3.2 7.2 + - - +
97A MET* 3.0 22.3 + - - +
109A PHE* 3.5 33.4 - - + -
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Residues in contact with ILE 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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90A LEU* 3.2 10.5 + - + +
91A LEU* 3.2 40.6 + - + +
93A MET* 1.3 76.7 - - - +
95A PRO* 1.3 69.5 - - + +
97A MET* 3.0 17.8 + - - +
98A TYR* 3.2 35.1 + - + -
132A ALA* 3.6 24.9 - - + +
133A ALA* 4.1 19.1 - - + -
135A GLN* 6.3 0.2 - - - +
136A THR* 4.1 4.5 - - + -
91B LEU* 4.6 14.4 - - + +
94B ILE* 5.3 14.4 - - + -
132B ALA* 5.8 1.1 - - + -
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Residues in contact with PRO 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 LEU 4.0 4.5 - - - +
92A LEU* 3.7 11.7 - - - +
93A MET 3.3 5.2 - - - -
94A ILE* 1.3 94.4 - - + +
96A ASN* 1.4 59.0 - - - +
98A TYR* 3.3 13.6 + - + +
99A LYS* 3.4 13.0 + - - +
88B GLN* 4.6 8.4 + - - +
91B LEU* 4.2 36.6 - - + +
92B LEU* 4.3 13.5 - - + -
117B ALA 4.6 0.5 - - - +
868B LEU* 3.7 22.6 - - + +
870B GLU* 3.9 14.4 - - - +
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Residues in contact with ASN 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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65A ALA 4.2 4.9 + - - -
68A ALA* 3.6 32.3 - - + +
69A GLY* 3.4 14.5 - - - +
72A HIS* 3.0 33.3 + - - +
92A LEU 5.5 0.4 + - - +
93A MET 3.2 2.3 + - - +
95A PRO* 1.4 76.8 - - - +
97A MET* 1.3 59.8 + - - +
99A LYS* 3.0 4.7 + - - +
100A ILE* 2.8 36.4 + - + +
867B SER* 3.1 5.4 + - - -
868B LEU* 3.5 13.8 - - - +
870B GLU* 6.1 0.2 - - - +
871B ASP* 2.9 25.5 + - - +
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Residues in contact with MET 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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90A LEU* 3.6 22.2 - - - -
93A MET* 3.0 20.7 + - - +
94A ILE* 3.0 17.6 + - - +
96A ASN* 1.3 76.5 - - - +
98A TYR* 1.3 62.4 + - - +
100A ILE* 4.5 0.9 - - - -
101A SER* 3.0 28.6 + - - -
109A PHE* 3.6 21.3 - - + -
133A ALA* 3.8 12.8 - - + +
136A THR* 3.6 26.2 - - - +
138A PHE* 3.5 36.8 - - + -
168A MET* 3.4 27.4 - - + -
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Residues in contact with TYR 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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94A ILE* 3.2 43.9 + - + -
95A PRO 3.5 7.0 - - - +
97A MET* 1.3 78.4 - - - +
99A LYS* 1.3 56.2 + - - +
101A SER* 3.3 1.7 + - - -
102A GLY* 2.8 26.9 + - - -
135A GLN* 3.3 42.7 - - + +
136A THR* 3.7 22.4 + - + -
229A ARG* 4.6 17.0 - - - -
91B LEU* 4.0 16.2 - - + -
116B ILE* 3.5 27.8 - - + -
117B ALA 3.6 16.2 - - - +
118B ALA* 3.5 11.4 - - + +
128B GLN* 4.4 8.0 + - + -
132B ALA* 3.4 17.8 - - + +
331B LYS 5.9 0.2 - - - -
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Residues in contact with LYS 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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72A HIS* 3.7 24.0 - - + +
95A PRO 3.4 4.1 + - - +
96A ASN* 3.0 9.2 + - - +
98A TYR* 1.3 76.7 - - - +
100A ILE* 1.3 60.1 + - - +
103A GLU* 2.9 46.7 + - - +
217A GLY* 3.9 15.8 - - - -
117B ALA* 3.5 32.6 - - - +
118B ALA 3.7 18.6 + - - +
120B ALA 4.9 0.6 - - - -
121B LEU 4.7 6.1 - - - +
866B ASN* 3.0 28.9 + - - +
867B SER 3.0 18.6 + - - +
868B LEU* 4.0 18.4 - - + -
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Residues in contact with ILE 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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68A ALA 4.2 5.4 - - - +
71A VAL* 4.2 17.5 - - + -
72A HIS* 3.9 30.1 - - + -
75A LEU* 4.1 18.6 - - + -
96A ASN* 2.8 28.6 + - + +
97A MET 4.0 3.4 - - - +
99A LYS* 1.3 71.5 - - - +
101A SER* 1.3 60.1 + - - +
103A GLU 3.6 0.5 + - - -
104A LEU 3.3 3.3 + - - -
105A LEU* 3.1 39.3 + - + +
107A GLY* 4.7 1.6 - - - +
109A PHE* 3.9 26.7 - - + -
138A PHE* 3.9 7.0 - - + -
166A PRO* 3.8 23.9 - - + +
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Residues in contact with SER 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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97A MET 3.0 12.4 + - - -
98A TYR 3.3 3.1 + - - -
100A ILE* 1.3 76.6 - - - +
102A GLY* 1.3 68.5 + - - +
104A LEU* 3.0 23.4 + - - +
136A THR 2.6 24.1 + - - -
137A GLY* 3.5 28.3 - - - -
138A PHE* 4.2 0.7 - - - -
166A PRO* 3.6 19.3 - - - -
229A ARG* 5.7 2.8 + - - -
232A ALA* 5.7 0.7 - - - +
236A TYR* 3.7 10.3 + - - -
333B PRO* 5.9 0.2 - - - +
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Residues in contact with GLY 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 TYR 2.8 20.7 + - - -
99A LYS 3.2 1.5 + - - -
101A SER* 1.3 78.1 + - - +
103A GLU* 1.3 58.8 + - - +
104A LEU* 3.3 2.5 + - - +
229A ARG* 5.1 4.7 - - - -
232A ALA* 5.6 1.6 - - - +
118B ALA* 3.8 17.7 - - - -
119B HIS* 3.6 23.3 - - - +
661B ALA 3.8 4.2 - - - +
662B ASP* 3.7 8.3 - - - -
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Residues in contact with GLU 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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72A HIS* 2.8 31.7 + - - -
99A LYS* 2.9 31.7 + - - +
102A GLY* 1.3 77.8 - - - +
104A LEU* 1.3 71.3 + - - +
105A LEU* 3.4 13.3 + - + +
206A LYS* 4.4 1.4 + - - -
216A ARG* 2.8 43.4 + - + +
217A GLY* 4.1 16.0 + - - +
118B ALA 4.3 7.4 - - - +
119B HIS* 4.9 2.2 - - - +
662B ASP* 3.4 31.8 - - + +
866B ASN 4.3 2.8 - - - +
875B TYR* 4.7 0.2 + - - -
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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