Contacts of the helix formed by residues 86 - 106 (chain A) in PDB entry 3KAV
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 TRP 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.8 11.2 - - + +
84A SER* 3.1 12.1 + - - +
85A PRO* 1.3 85.0 - - + +
87A ALA* 1.3 64.2 + - - +
88A PRO* 3.3 4.0 - - + -
89A ALA* 3.2 28.6 + - + +
90A ALA 3.3 8.5 + - - -
68B ASP* 3.2 46.0 + - - +
71B ASP* 4.4 9.4 - - + -
72B LEU* 3.6 30.6 - - + +
75B LEU* 5.7 1.4 - - + +
93B LEU* 4.4 18.8 - - + -
97B TYR* 3.3 44.6 - + - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 4.0 9.4 - - - +
76A ALA* 5.3 0.4 - - - -
79A LEU* 3.8 23.8 - - - +
80A MSE 3.9 26.5 - - + -
84A SER* 3.2 18.4 + - - +
86A TRP* 1.3 77.6 - - - +
88A PRO* 1.3 69.7 - - + +
90A ALA* 3.1 4.7 + - - +
91A CYS* 2.9 27.2 + - - -
129A LEU* 6.1 1.1 - - + -
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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
----------------------------------------------------------
84A SER 4.4 0.7 - - - +
85A PRO* 3.1 19.5 - - + +
86A TRP* 4.3 1.1 - - + -
87A ALA* 1.3 95.4 - - + +
89A ALA* 1.3 58.4 + - + +
91A CYS* 3.2 10.0 + - + +
92A GLU* 2.9 29.0 + - - +
129A LEU* 3.1 35.4 - - + +
130A LEU* 4.4 7.2 - - - +
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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
----------------------------------------------------------
86A TRP* 3.2 32.0 + - + +
87A ALA 3.2 0.4 - - - -
88A PRO* 1.3 81.2 - - + +
90A ALA* 1.3 62.8 + - - +
92A GLU* 3.3 9.4 + - - +
93A LEU* 3.3 25.3 + - - +
72B LEU* 5.7 1.1 - - + -
75B LEU* 4.8 12.6 - - + -
93B LEU* 5.9 5.2 - - + -
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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
----------------------------------------------------------
72A LEU* 5.0 3.5 - - + +
75A LEU* 4.8 1.8 - - + -
76A ALA* 3.9 21.4 - - + +
79A LEU* 3.4 31.6 - - + -
86A TRP 3.3 1.4 + - - -
87A ALA 3.1 7.2 + - - +
89A ALA* 1.3 80.0 - - - +
91A CYS* 1.3 58.0 + - - +
93A LEU* 3.3 3.0 + - - +
94A ALA* 2.9 29.8 + - - +
75B LEU* 4.5 20.6 - - + +
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A CYS* 4.2 7.9 - - - -
76A ALA* 4.4 10.1 - - - -
80A MSE 3.8 38.6 - - - -
87A ALA 2.9 25.1 + - - -
88A PRO* 3.2 11.4 + - + +
90A ALA* 1.3 73.6 - - - +
92A GLU* 1.3 60.1 + - - +
94A ALA* 4.2 6.1 - - - -
95A ALA* 2.8 32.2 + - - +
122A PHE* 5.2 0.7 - - - -
126A CYS* 3.6 22.8 - - + -
129A LEU* 5.2 4.7 - - + -
130A LEU* 4.6 4.5 - - + -
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Residues in contact with GLU 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 PRO 2.9 13.7 + - - +
89A ALA* 3.3 14.1 - - - +
90A ALA 3.1 0.4 - - - -
91A CYS* 1.3 77.7 - - - +
93A LEU* 1.3 68.2 + - + +
95A ALA* 3.7 4.9 - - - +
96A ARG* 2.9 49.5 + - - +
130A LEU* 3.7 32.1 - - + +
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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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72A LEU* 4.2 13.9 - - + -
89A ALA 3.3 8.5 + - - +
90A ALA 3.3 5.6 + - - +
92A GLU* 1.3 85.3 - - + +
94A ALA* 1.3 63.2 + - - +
96A ARG* 3.1 23.6 + - - +
97A TYR* 3.1 22.1 + - + -
75B LEU* 3.8 27.6 - - + -
79B LEU* 3.7 28.5 - - + -
86B TRP* 3.8 40.6 - - + +
90B ALA* 5.2 2.2 - - + -
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Residues in contact with ALA 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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69A CYS* 5.0 1.7 - - - -
72A LEU* 4.0 36.7 - - + +
73A CYS* 4.3 2.0 - - - +
76A ALA* 4.2 2.5 - - + -
90A ALA 2.9 18.4 + - - +
91A CYS* 3.9 2.9 - - - +
93A LEU* 1.3 73.8 - - - +
95A ALA* 1.3 61.2 + - - +
97A TYR* 3.2 3.2 + - - +
98A ALA* 2.7 30.5 + - - +
122A PHE* 3.7 25.7 - - + -
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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 CYS 2.8 21.3 + - - +
92A GLU* 3.7 7.6 - - - +
94A ALA* 1.3 75.3 - - - +
96A ARG* 1.3 54.5 + - - +
98A ALA* 3.5 7.0 - - - +
99A LEU* 2.7 38.4 + - - +
122A PHE* 4.0 5.6 - - - -
123A VAL* 3.8 18.5 - - + +
126A CYS* 4.1 17.7 - - + -
130A LEU* 5.6 5.8 - - + -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 2.9 39.4 + - - +
93A LEU* 3.1 21.9 + - - +
95A ALA* 1.3 79.5 - - - +
97A TYR* 1.3 62.8 + - + +
99A LEU* 3.2 5.7 + - - +
100A ALA* 2.9 29.7 + - - +
86B TRP* 3.2 44.8 - - + +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 4.7 6.4 - + - +
68A ASP* 3.3 38.4 - - + -
69A CYS* 3.9 16.8 - - - +
72A LEU* 3.2 31.4 - - + -
93A LEU* 3.1 15.3 + - + -
94A ALA 3.9 3.6 - - - +
96A ARG* 1.3 83.0 - - + +
98A ALA* 1.3 57.4 + - - +
100A ALA* 3.8 8.4 - - + +
101A CYS* 2.9 30.3 + - - +
79B LEU* 5.0 2.5 - - + -
82B ARG* 5.7 3.4 - - + -
84B SER* 2.7 39.3 + - - -
85B PRO* 3.6 4.9 - - - +
86B TRP* 3.5 28.5 - + - -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 3.5 23.7 - - - -
94A ALA 2.7 20.4 + - - +
95A ALA 3.5 4.3 - - - +
97A TYR* 1.3 71.2 - - - +
99A LEU* 1.3 60.3 + - - +
101A CYS* 3.2 1.7 + - - +
102A ALA 2.9 25.5 + - - -
119A CYS* 3.3 20.0 - - + +
122A PHE* 3.8 17.0 - - + -
123A VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 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 2.7 21.9 + - - +
96A ARG* 3.5 6.1 - - - +
98A ALA* 1.3 74.4 - - - +
100A ALA* 1.3 55.5 + - - +
102A ALA* 3.4 3.4 + - - +
103A GLU* 2.8 74.9 + - + +
120A ARG* 3.6 26.5 - - + +
123A VAL* 3.9 27.5 - - + +
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Residues in contact with ALA 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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65A HIS* 4.0 17.5 - - + +
96A ARG 2.9 16.1 + - - +
97A TYR* 3.8 10.1 - - + +
99A LEU* 1.3 73.1 - - - +
101A CYS* 1.3 64.3 + - - +
103A GLU* 3.4 12.4 + - - +
104A ARG* 2.9 41.3 + - - +
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Residues in contact with CYS 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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48A CYS* 4.2 2.0 - - - -
65A HIS* 4.1 15.9 - - + -
66A ALA* 3.5 31.0 - - - -
69A CYS* 4.0 6.7 - - + -
97A TYR 2.9 18.7 + - - +
98A ALA 3.4 4.9 - - - +
100A ALA* 1.3 77.1 - - - +
102A ALA* 1.3 53.7 + - - +
105A CYS* 2.7 43.8 + - - +
115A CYS* 3.8 17.5 - - - -
119A CYS* 3.8 21.3 - - - -
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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 ALA 2.9 17.1 + - - +
99A LEU* 3.6 4.7 - - - +
101A CYS* 1.3 77.0 - - - +
103A GLU* 1.3 62.1 + - - +
104A ARG 3.2 0.9 + - - -
106A ASP* 3.3 28.8 + - - +
116A ALA* 3.8 21.7 - - - +
119A CYS* 4.1 2.2 - - + +
120A ARG* 3.6 44.5 + - + +
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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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99A LEU* 2.8 47.0 + - + +
100A ALA* 3.6 9.3 - - - +
101A CYS 3.4 0.2 - - - -
102A ALA* 1.3 75.0 - - - +
104A ARG* 1.3 80.0 + - - +
106A ASP* 4.9 1.6 - - - +
120A ARG* 3.9 16.8 - - - +
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Residues in contact with ARG 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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61A GLU* 3.6 31.8 + - - +
62A GLN* 3.0 20.2 + - + +
65A HIS* 3.6 32.0 + - + +
100A ALA* 2.9 39.6 + - - +
101A CYS 3.9 1.6 - - - +
103A GLU* 1.3 106.8 + - - +
105A CYS* 1.3 66.2 + - - +
106A ASP 3.6 4.0 + - - +
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Residues in contact with CYS 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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51A TYR* 3.5 22.5 - - + +
62A GLN* 3.4 51.4 + - - +
65A HIS* 4.6 1.3 - - - -
101A CYS* 2.7 37.1 + - - +
102A ALA* 5.3 0.4 - - - -
104A ARG* 1.3 74.4 - - - +
106A ASP* 1.3 65.4 + - - +
112A GLU* 3.2 27.3 - - - +
115A CYS* 4.5 8.5 - - + -
116A ALA* 5.0 1.1 - - - +
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Residues in contact with ASP 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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62A GLN* 5.1 2.1 + - - -
102A ALA 3.3 18.4 + - - +
103A GLU 5.2 1.5 + - - +
104A ARG 3.6 5.4 - - - +
105A CYS* 1.3 79.0 - - - +
107A GLY* 1.3 69.7 + - - +
112A GLU* 3.8 7.3 - - - +
113A ARG* 3.5 21.2 - - - +
116A ALA* 3.4 17.2 - - + +
120A ARG* 4.8 9.3 + - - +
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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
------------------------------------------------------------
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