Contacts of the helix formed by residues 87 - 104 (chain A) in PDB entry 4KN1
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 GLU 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.7 9.1 + - - +
86A MET* 1.3 73.2 - - - +
88A PRO* 1.3 71.7 - - + +
89A ALA* 3.2 8.1 - - + +
90A CYS* 2.8 10.3 + - + +
91A LYS* 2.7 31.6 + - - +
139A ASP 5.3 0.2 - - - +
142A THR* 3.5 35.2 - - - +
143A SER* 3.3 16.7 + - - +
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET 3.6 4.0 - - - +
87A GLU* 1.3 97.2 - - + +
89A ALA* 1.3 62.7 + - - +
91A LYS* 4.2 9.0 - - + -
92A ARG* 3.0 28.7 + - - +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.2 6.0 - - + -
88A PRO* 1.3 79.1 - - - +
90A CYS* 1.3 56.9 + - - +
92A ARG* 3.0 40.5 + - - +
93A HIS* 3.1 16.6 + - - -
139A ASP* 3.5 17.9 - - + +
142A THR* 6.2 0.2 - - - +
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Residues in contact with CYS 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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86A MET* 3.9 13.0 - - + -
87A GLU* 2.8 9.4 + - + +
89A ALA* 1.3 78.7 - - - +
91A LYS* 1.3 66.9 + - - +
92A ARG 3.2 2.0 - - - -
93A HIS* 3.0 21.1 + - - +
94A PHE* 3.6 19.4 + - - -
139A ASP 3.5 11.9 - - - +
140A CYS* 2.0 50.9 - - - -
143A SER* 3.6 17.7 - - - +
172A PHE* 4.4 0.9 - - - -
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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
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69A HIS 5.8 1.1 - - - +
71A ASP* 2.7 38.0 + - - +
80A TRP* 4.0 20.2 - - + -
81A ASP* 3.0 28.6 + - - -
85A LYS* 5.9 0.6 - - - +
86A MET* 3.6 30.7 + - - -
87A GLU 2.7 18.1 + - - +
88A PRO* 3.9 9.0 - - + +
90A CYS* 1.3 74.0 - - - +
92A ARG* 1.3 62.2 + - - +
94A PHE* 3.1 4.2 + - - +
95A ILE* 2.9 37.5 + - + +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 2.9 31.6 + - - +
88A PRO 3.0 15.0 + - - +
89A ALA* 3.0 34.7 + - - +
91A LYS* 1.3 76.6 - - - +
93A HIS* 1.3 64.4 + - + +
95A ILE* 3.5 4.2 + - - +
96A GLN* 2.9 25.3 + - - +
135A ARG* 3.5 19.9 - - - +
139A ASP* 3.0 28.3 + - - -
207A TRP* 3.7 18.3 - - + -
304A CL 3.7 21.4 - - - +
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA 3.1 23.3 + - - -
90A CYS* 3.0 9.3 + - - +
92A ARG* 1.3 83.7 + - + +
94A PHE* 1.3 61.0 + - - +
96A GLN* 3.2 4.2 + - - -
97A ASP* 2.8 30.4 + - - +
132A ASP 5.3 1.0 + - - -
135A ARG* 3.7 21.7 + - + -
136A TRP* 3.3 45.2 - + + +
139A ASP* 2.6 38.7 + - + +
206A MET* 3.4 7.4 - - + +
207A TRP* 3.3 29.2 + + - -
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Residues in contact with PHE 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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80A TRP* 3.9 28.6 + + + +
86A MET* 3.6 24.7 - - + -
90A CYS* 3.6 28.0 - - - -
91A LYS* 3.1 6.3 + - - +
93A HIS* 1.3 77.8 - - - +
95A ILE* 1.3 57.8 + - - +
97A ASP* 3.6 8.3 + - - +
98A THR* 2.9 31.4 + - - -
136A TRP* 3.6 22.4 - + - -
150A TRP* 3.2 38.1 - + - -
172A PHE* 3.6 15.5 - + - -
182A LEU* 4.7 2.2 - - + -
186A LEU* 3.6 26.5 - - + -
187A TRP* 4.9 6.1 - + - -
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Residues in contact with ILE 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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50A GLN* 3.6 29.4 - - + +
68A LEU* 3.9 12.3 - - + +
69A HIS* 3.8 42.6 - - + +
80A TRP* 3.6 25.1 - - + -
91A LYS* 2.9 35.0 + - + +
92A ARG* 3.7 5.2 - - - +
94A PHE* 1.3 76.2 - - - +
96A GLN* 1.3 66.3 + - - +
98A THR* 3.2 5.7 + - - -
99A CYS* 3.0 21.1 + - - -
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Residues in contact with GLN 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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50A GLN* 3.1 32.1 + - - +
53A PRO* 5.3 4.0 - - - +
54A TRP* 3.4 22.6 - - - -
92A ARG 2.9 17.8 + - - +
93A HIS 3.5 4.9 - - - +
95A ILE* 1.3 77.0 - - - +
97A ASP* 1.3 62.7 + - - +
99A CYS* 3.1 7.4 + - - +
100A LEU* 3.0 22.0 + - - +
206A MET* 2.9 32.5 + - + +
207A TRP* 3.5 50.7 - - + +
208A PHE 4.6 2.6 + - - +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS 2.8 20.6 + - - +
94A PHE* 3.7 8.5 - - - +
96A GLN* 1.3 74.0 - - - +
98A THR* 1.3 55.5 + - - +
100A LEU* 3.4 2.4 + - - +
101A TYR* 3.0 26.7 + - - +
136A TRP* 3.7 21.9 - - + -
187A TRP* 3.1 14.3 + - - -
191A TYR* 2.6 38.7 + - - -
206A MET* 4.0 13.6 - - - +
301A 04J 2.9 29.5 + - - -
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.8 30.3 - - + +
75A LEU* 4.5 5.4 - - + -
76A TYR* 5.6 4.0 - - + -
80A TRP* 3.9 14.4 + - + -
94A PHE 2.9 18.5 + - - -
95A ILE* 3.2 6.7 + - - -
97A ASP* 1.3 73.4 - - - +
99A CYS* 1.3 60.4 + - - +
101A TYR* 4.4 1.6 - - + -
102A GLU* 2.9 45.0 + - + +
187A TRP* 5.9 0.2 - - - -
301A 04J 4.2 17.0 + - - +
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Residues in contact with CYS 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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50A GLN* 3.8 12.1 - - - -
51A CYS* 2.0 59.2 - - + -
54A TRP* 3.7 19.1 - - + -
68A LEU* 3.8 7.8 - - - +
95A ILE 3.0 16.7 + - - -
96A GLN* 3.3 10.1 - - - +
98A THR* 1.3 75.1 - - - +
100A LEU* 1.3 54.0 + - - +
103A CYS* 2.7 41.4 + - - +
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Residues in contact with LEU 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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54A TRP* 3.8 23.7 - - + -
96A GLN 3.0 12.0 + - - +
97A ASP* 3.6 8.3 - - - +
98A THR 3.2 0.2 - - - -
99A CYS* 1.3 73.9 - - - +
101A TYR* 1.3 66.2 + - - +
104A SER* 3.0 50.4 + - - +
107A LEU* 4.1 14.1 - - + +
128A LEU* 5.4 0.2 - - + -
191A TYR* 3.2 34.5 - - + +
204A ILE* 4.2 25.1 - - + -
205A GLN 4.5 5.2 - - - +
206A MET* 4.1 16.4 - - + +
302A K 4.0 8.3 - - - -
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Residues in contact with TYR 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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32A MET* 3.2 31.7 - - + +
34A ALA* 4.0 4.6 - - + +
37A HIS* 3.0 28.2 + + - -
76A TYR* 3.5 11.9 + + - -
97A ASP* 3.0 17.8 + - - +
98A THR* 3.8 4.3 - - + +
100A LEU* 1.3 80.3 - - - +
102A GLU* 1.3 87.8 + - + +
104A SER 4.6 1.0 + - - +
107A LEU* 5.0 0.4 - - - -
118A TRP* 4.3 4.8 - + - -
119A ARG* 2.8 32.0 + - - -
122A ARG* 5.4 0.7 - - + -
123A PHE* 3.7 25.5 - + - -
191A TYR* 5.6 0.2 + - - -
301A 04J 3.2 58.8 - + - +
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Residues in contact with GLU 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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36A HIS* 3.8 19.3 - - - +
37A HIS* 3.6 24.7 + - - -
59A CYS* 3.4 12.5 - - - +
60A CYS* 3.4 21.0 - - + +
64A THR* 4.3 7.5 - - + +
68A LEU* 4.4 3.8 - - + -
75A LEU* 4.3 14.1 - - + -
76A TYR* 2.5 40.9 + - - -
98A THR* 2.9 35.5 + - + +
101A TYR* 1.3 88.5 - - + +
103A CYS* 1.3 63.4 + - - +
104A SER 3.8 0.2 - - - -
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Residues in contact with CYS 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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47A LEU* 4.7 0.7 - - - -
51A CYS* 4.2 21.5 - - - -
54A TRP* 3.8 22.4 - - + -
58A ALA* 3.3 9.9 - - + +
59A CYS 2.8 21.4 + - - -
60A CYS* 2.0 49.8 - - - +
68A LEU* 5.0 1.8 - - - -
99A CYS 2.7 26.7 + - - +
102A GLU* 1.3 77.6 - - - +
104A SER* 1.3 62.9 + - - +
105A PRO* 3.4 2.6 - - - +
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Residues in contact with SER 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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30A VAL 4.1 2.1 - - - +
31A CYS* 5.1 0.3 - - - -
37A HIS* 4.9 4.9 + - - -
54A TRP* 3.9 4.9 - - - +
59A CYS* 3.2 13.8 - - - +
99A CYS 4.0 0.4 + - - -
100A LEU* 3.0 36.8 + - - -
101A TYR 4.6 0.9 + - - +
102A GLU 3.8 0.6 - - - -
103A CYS* 1.3 76.6 - - - +
105A PRO* 1.3 62.8 - - - +
106A ASN* 3.0 17.2 + - - +
107A LEU* 3.3 26.7 + - - +
123A PHE* 5.5 2.1 - - - -
302A K 3.3 12.1 - - - -
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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
------------------------------------------------------------
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