Contacts of the helix formed by residues 90 - 108 (chain A) in PDB entry 6KI3
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 SER 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL 4.0 5.2 - - - -
85A PRO 3.4 21.2 + - - -
87A SER* 3.2 34.7 + - - -
88A ARG 3.1 6.6 + - - -
89A ARG* 1.3 72.5 - - - +
91A ALA* 1.3 59.9 + - - +
92A PHE 3.3 2.7 - - - -
93A VAL* 3.6 7.4 - - - -
94A THR* 2.9 29.9 + - - -
130A LYS* 4.3 14.7 - - - +
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Residues in contact with ALA 91 (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 ARG* 3.6 2.0 - - - +
90A SER* 1.3 78.3 + - - +
92A PHE* 1.3 63.0 + - - +
93A VAL 3.4 0.2 + - - -
94A THR* 4.6 2.0 - - - -
95A HIS* 3.4 22.3 + - - +
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Residues in contact with PHE 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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89A ARG 5.1 3.0 + - - +
90A SER 3.3 0.2 - - - -
91A ALA* 1.3 79.3 - - - +
93A VAL* 1.3 64.4 + - + +
95A HIS* 4.2 4.6 + - - +
96A PHE* 3.4 20.4 + - - +
9E G 3.8 42.8 - - + +
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Residues in contact with VAL 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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82A LEU* 3.2 30.3 - - + +
83A ASP* 4.0 5.1 - - - +
84A VAL 3.4 29.6 - - - +
85A PRO* 4.2 1.6 - - + -
87A SER* 4.3 5.6 - - - +
89A ARG 4.2 15.7 - - - +
90A SER* 3.2 10.7 + - - +
91A ALA 3.2 1.0 - - - -
92A PHE* 1.3 79.2 - - + +
94A THR* 1.3 65.9 + - - +
96A PHE* 3.2 14.9 + - - +
97A ILE* 3.2 15.8 + - + +
9E G 5.4 7.4 - - + -
10E G 4.7 13.0 - - - -
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Residues in contact with THR 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 PRO* 3.8 27.7 + - - +
90A SER 2.9 17.1 + - - -
91A ALA* 4.6 2.2 - - - -
93A VAL* 1.3 77.0 - - - +
95A HIS* 1.3 63.8 + - - +
97A ILE* 3.2 10.8 + - - +
98A GLN* 3.1 20.9 + - + +
130A LYS* 3.3 41.1 - - + +
131A ILE* 3.9 15.1 - - + +
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Residues in contact with HIS 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 ALA 3.4 16.9 + - - +
92A PHE* 4.2 5.9 + - - +
93A VAL 3.3 0.4 - - - -
94A THR* 1.3 81.6 - - - +
96A PHE* 1.3 62.0 + - - +
98A GLN* 3.1 21.5 + - + +
99A GLN* 3.2 43.1 + - + +
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Residues in contact with PHE 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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47A ALA* 3.6 16.4 - - + -
52A ALA* 3.3 39.0 - - + -
53A VAL* 3.4 22.7 - - - -
54A ILE* 3.7 15.0 - - + -
80A THR* 3.7 17.7 - - + -
82A LEU* 6.5 0.7 - - + -
83A ASP* 3.6 11.4 - - - +
92A PHE 3.4 12.7 + - - +
93A VAL* 3.2 11.9 + - - +
95A HIS* 1.3 76.9 + - - +
97A ILE* 1.3 63.7 + - - +
99A GLN* 3.1 32.3 + - - +
100A GLU* 3.2 35.7 + - + +
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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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83A ASP* 3.5 40.2 - - + +
85A PRO* 3.6 33.7 - - + -
93A VAL* 3.2 15.6 + - + +
94A THR* 3.2 8.9 + - - +
96A PHE* 1.3 74.8 - - - +
98A GLN* 1.3 62.7 + - - +
100A GLU* 3.3 9.4 + - - +
101A LEU* 3.0 31.4 + - + +
112A LEU* 4.0 19.1 - - + -
114A LEU* 3.9 9.6 - - + -
131A ILE* 4.0 20.4 - - + -
139A ILE* 5.2 0.4 - - + -
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Residues in contact with GLN 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 THR* 3.1 13.6 + - + +
95A HIS* 3.1 19.5 + - + +
97A ILE* 1.3 78.5 - - - +
99A GLN* 1.3 61.7 + - + +
101A LEU* 3.6 3.4 + - - +
102A LEU* 3.2 23.6 + - - +
130A LYS 5.2 0.7 - - - +
131A ILE* 3.5 13.8 - - - +
132A LYS* 2.9 50.4 + - - +
133A PRO 4.5 0.4 + - - -
134A VAL* 4.0 17.6 - - - +
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Residues in contact with GLN 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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54A ILE* 4.2 23.6 - - + +
95A HIS* 3.2 43.2 + - + +
96A PHE* 3.1 26.6 + - - +
98A GLN* 1.3 75.2 - - + +
100A GLU* 1.3 59.1 + - - +
102A LEU* 3.3 5.7 + - - +
103A ILE* 2.9 37.8 + - + +
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Residues in contact with GLU 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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46A ILE* 3.9 19.1 - - + +
47A ALA* 3.6 16.0 + - + +
54A ILE* 4.1 17.7 - - + -
78A HIS 4.5 1.9 - - - +
79A GLY* 3.9 6.9 - - - -
80A THR* 3.8 9.2 + - - +
83A ASP* 2.8 29.1 - - - +
96A PHE* 3.2 29.9 + - - +
97A ILE* 3.7 9.2 - - - +
99A GLN* 1.3 79.6 - - - +
101A LEU* 1.3 57.8 + - - +
103A ILE* 3.1 4.7 + - - +
104A CYS* 2.8 35.4 + - - -
112A LEU* 4.0 17.8 - - + +
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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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97A ILE* 3.0 25.7 + - + +
98A GLN* 4.0 8.1 - - - +
100A GLU* 1.3 74.3 - - - +
102A LEU* 1.3 62.2 + - - +
104A CYS* 3.3 13.9 + - - +
105A LYS 3.3 9.5 + - - -
112A LEU* 3.8 27.1 - - + -
131A ILE* 3.6 30.5 - - + -
132A LYS 4.5 5.4 - - - +
133A PRO* 5.6 1.1 - - + -
134A VAL* 3.6 29.8 - - + +
137A VAL* 3.8 24.9 - - + +
139A ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 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 GLN* 3.2 18.8 + - + +
99A GLN* 3.7 5.8 - - - +
100A GLU 3.2 0.2 - - - -
101A LEU* 1.3 75.7 - - - +
103A ILE* 1.3 63.9 + - + +
105A LYS* 3.3 6.5 + - - +
106A GLU* 3.2 24.2 + - - +
134A VAL* 4.1 13.6 - - + +
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Residues in contact with ILE 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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46A ILE* 3.8 18.2 - - + -
54A ILE* 3.7 43.5 - - + -
56A ILE* 4.0 18.4 - - + -
61A LYS* 4.2 25.6 - - - +
99A GLN* 2.9 24.9 + - + +
100A GLU* 3.5 5.4 - - - +
102A LEU* 1.3 77.2 - - + +
104A CYS* 1.3 64.5 + - - +
106A GLU* 3.1 17.3 + - - +
107A VAL* 3.2 20.2 + - + +
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Residues in contact with CYS 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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46A ILE* 3.9 17.3 - - - -
77A ALA* 3.9 9.9 - - - -
100A GLU 2.8 29.9 + - - +
101A LEU* 3.6 8.1 - - - +
102A LEU 3.2 0.2 - - - -
103A ILE* 1.3 73.7 - - - +
105A LYS* 1.3 56.6 + - - +
107A VAL* 3.4 3.0 + - - +
108A GLY 3.0 8.3 + - - -
109A ILE* 2.8 58.6 + - + +
111A GLY 4.1 6.1 - - - -
112A LEU* 4.4 7.2 - - - -
137A VAL* 3.8 18.4 - - + -
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Residues in contact with LYS 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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65A LEU* 5.6 0.7 - - - +
101A LEU 3.3 3.4 + - - -
102A LEU* 3.3 6.5 + - - +
103A ILE 3.3 0.2 - - - -
104A CYS* 1.3 77.6 - - - +
106A GLU* 1.3 67.5 + - + +
107A VAL 3.4 0.3 + - - -
108A GLY* 3.5 8.9 + - - +
109A ILE 4.9 0.7 - - - -
134A VAL* 3.6 33.0 - - + +
135A GLU* 3.4 29.2 - - - +
136A GLY* 5.5 0.7 - - - -
137A VAL* 3.7 8.4 - - + +
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Residues in contact with GLU 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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61A LYS* 4.6 16.5 - - + +
65A LEU* 3.9 18.4 - - - +
102A LEU 3.2 15.8 + - - +
103A ILE* 3.1 13.3 + - - +
105A LYS* 1.3 81.0 - - + +
107A VAL* 1.3 64.9 + - + +
108A GLY 3.9 0.2 + - - -
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Residues in contact with VAL 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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46A ILE* 5.7 0.2 - - + -
56A ILE* 4.5 6.3 - - + -
61A LYS* 3.4 48.7 - - + +
64A LEU* 3.9 14.4 - - + -
65A LEU* 3.5 21.9 - - - +
68A ILE* 3.3 17.7 - - - +
103A ILE* 3.2 20.6 + - + +
104A CYS* 3.6 7.0 - - - +
106A GLU* 1.3 80.2 - - + +
108A GLY* 1.3 59.5 + - - +
109A ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 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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65A LEU* 3.8 11.8 - - - +
68A ILE* 3.9 20.8 - - - +
75A VAL 4.8 0.7 + - - +
104A CYS 3.0 4.5 + - - -
105A LYS* 3.5 8.0 + - - -
106A GLU 3.5 3.0 - - - -
107A VAL* 1.3 78.5 - - - +
109A ILE* 1.3 63.3 + - - +
110A LYS* 3.6 15.7 + - - +
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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