Contacts of the helix formed by residues 81 - 100 (chain A) in PDB entry 4UY1
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 ASN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.6 5.4 + - - -
79A ALA* 3.4 6.3 - - - +
80A GLU* 1.3 77.2 - - - +
82A LYS* 1.3 63.0 + - - +
83A CYS* 3.2 7.9 + - - +
84A GLN* 2.9 39.1 + - - +
85A GLU* 3.5 15.1 + - - +
57B GLY 3.5 9.0 - - - +
63B GLU* 2.8 28.5 + - - +
81B ASN* 3.4 21.7 - - - +
83B CYS* 3.7 24.9 - - - +
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Residues in contact with LYS 82 (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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81A ASN* 1.3 71.9 - - - +
83A CYS* 1.3 68.5 + - - +
85A GLU* 3.0 31.3 + - + +
86A LEU* 2.9 39.9 + - + +
57B GLY 4.4 3.0 + - - -
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Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 5.3 0.9 - - - -
57A GLY 3.9 2.7 - - - -
58A CYS* 2.1 56.8 - - + -
63A GLU* 3.3 20.0 - - - +
81A ASN* 3.2 8.1 + - - +
82A LYS* 1.3 78.7 - - - +
84A GLN* 1.3 62.8 + - - +
86A LEU* 3.2 2.2 + - - +
87A LEU* 2.9 30.9 + - + +
81B ASN* 3.8 19.7 - - - +
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Residues in contact with GLN 84 (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 GLU* 3.7 15.8 + - + +
64A ARG 3.6 26.4 + - - +
65A TYR* 3.9 15.8 - - + +
78A PRO 4.2 0.7 - - - +
79A ALA* 3.6 11.7 - - + -
80A GLU* 2.7 61.4 + - - +
81A ASN* 2.9 24.7 + - - +
82A LYS 3.3 0.2 - - - -
83A CYS* 1.3 75.9 - - - +
85A GLU* 1.3 62.6 + - - +
87A LEU* 4.0 5.1 - - - +
88A CYS* 3.1 25.5 + - - +
1133A PEG 4.1 12.3 - - - +
63B GLU* 4.8 1.4 + - - +
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Residues in contact with GLU 85 (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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76A CYS* 5.3 4.1 - - + +
79A ALA* 4.2 19.3 - - + +
81A ASN 3.5 7.6 + - - +
82A LYS* 3.0 55.5 + - + +
84A GLN* 1.3 76.6 - - - +
86A LEU* 1.3 64.6 + - + +
88A CYS* 3.5 4.6 + - - +
89A LYS* 3.0 47.6 + - - +
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Residues in contact with LEU 86 (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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52A ARG 5.9 0.7 - - - -
53A ALA* 4.7 11.2 - - + -
56A ALA* 4.1 24.9 - - + -
58A CYS* 4.2 14.6 - - - -
82A LYS* 2.9 35.2 + - + +
83A CYS* 3.8 4.9 - - - +
85A GLU* 1.3 79.1 - - + +
87A LEU* 1.3 67.4 + - + +
89A LYS* 3.2 22.1 + - + +
90A CYS* 2.9 30.2 + - - -
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Residues in contact with LEU 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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1A GLY 4.6 0.4 - - - +
50A TYR* 5.4 2.0 - - + -
53A ALA* 3.9 22.7 - - + -
58A CYS* 4.1 11.2 - - + -
59A SER 3.9 0.7 - - - +
60A PRO* 3.7 36.8 - - + +
63A GLU* 3.6 46.9 - - + +
65A TYR* 3.9 18.8 - - + -
83A CYS 2.9 22.4 + - - +
84A GLN* 4.0 1.3 - - - +
86A LEU* 1.3 76.6 - - + +
88A CYS* 1.3 63.1 + - - +
90A CYS* 3.2 8.4 + - - +
91A ASP* 3.1 28.0 + - - +
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Residues in contact with CYS 88 (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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8A THR* 5.5 0.2 - - - -
65A TYR* 3.4 38.9 - - + -
66A SER 5.3 0.2 - - - +
67A TRP* 4.1 7.2 - - - -
74A VAL* 4.3 6.1 - - - -
76A CYS* 2.0 55.0 - - + -
77A GLY 5.7 0.2 - - - +
84A GLN 3.1 16.4 + - - +
85A GLU* 3.9 3.1 - - - +
87A LEU* 1.3 78.1 - - - +
89A LYS* 1.3 56.6 + - - +
91A ASP* 4.1 0.2 - - - +
92A GLN* 2.9 32.2 + - - +
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Residues in contact with LYS 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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49A CYS* 5.0 1.6 - - - -
76A CYS* 4.8 4.0 - - + -
85A GLU* 3.0 38.7 + - - +
86A LEU* 3.4 24.5 - - + +
88A CYS* 1.3 74.1 - - - +
90A CYS* 1.3 67.8 + - - +
92A GLN* 3.7 13.5 - - - +
93A GLU* 2.9 26.0 + - - +
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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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46A HIS* 3.3 11.8 - - + -
49A CYS* 2.0 65.3 - - + -
50A TYR* 3.9 20.6 - - + -
53A ALA* 4.9 5.4 - - - -
86A LEU* 2.9 22.6 + - - -
87A LEU* 3.2 9.2 + - - +
89A LYS* 1.3 76.2 - - - +
91A ASP* 1.3 57.5 + - - +
93A GLU* 3.3 5.0 + - - +
94A ILE 3.1 22.3 + - - -
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Residues in contact with ASP 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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1A GLY 4.0 2.6 + - - +
5A LEU* 3.7 18.2 + - + -
8A THR* 3.5 18.3 + - - +
46A HIS* 2.8 19.9 + - - -
50A TYR* 2.7 31.6 + - - -
65A TYR* 2.7 38.6 + - - +
87A LEU* 3.1 9.3 + - - +
88A CYS 4.1 0.2 - - - +
90A CYS* 1.3 72.1 - - - +
92A GLN* 1.3 67.1 + - - +
94A ILE* 3.4 8.6 - - - +
95A ALA* 2.9 26.5 + - - +
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Residues in contact with GLN 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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8A THR* 4.8 1.6 - - - +
74A VAL* 2.7 52.5 + - + +
76A CYS* 3.9 8.3 - - - -
88A CYS 2.9 19.2 + - - +
89A LYS* 3.7 12.9 - - - +
91A ASP* 1.3 74.7 - - - +
93A GLU* 1.3 57.2 + - - +
95A ALA* 3.6 5.5 - - - +
96A ASN* 2.8 50.8 + - - +
1126A DMS 3.6 18.3 + - - -
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Residues in contact with GLU 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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45A GLY* 4.7 9.1 - - - +
46A HIS* 5.4 0.9 + - - -
49A CYS* 4.1 23.4 - - - +
52A ARG* 5.3 3.3 + - - -
89A LYS 2.9 18.7 + - - +
90A CYS 3.6 3.1 - - - +
91A ASP 3.2 0.2 - - - -
92A GLN* 1.3 78.3 - - - +
94A ILE* 1.3 58.5 + - - +
96A ASN* 3.4 7.2 + - - +
97A CYS* 2.9 32.0 + - + +
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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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5A LEU* 3.9 13.0 - - + -
9A VAL* 4.3 5.2 - - + -
42A CYS* 3.7 20.4 - - + +
43A CYS* 4.4 7.0 - - - -
46A HIS* 3.4 51.6 - - + +
90A CYS 3.1 7.3 + - - -
91A ASP 3.4 10.8 - - - +
93A GLU* 1.3 77.1 - - - +
95A ALA* 1.3 57.2 + - - +
97A CYS* 3.2 4.5 + - - +
98A LEU* 2.8 63.6 + - + +
1130A TJM 3.8 22.0 - - + +
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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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8A THR* 3.5 34.5 - - - +
9A VAL* 3.9 13.4 - - + +
12A VAL* 3.8 13.9 - - + +
13A GLY* 4.9 1.0 + - - -
74A VAL* 4.7 0.2 - - + -
91A ASP 2.9 19.3 + - - +
92A GLN* 3.6 6.1 - - - +
94A ILE* 1.3 77.0 - - - +
96A ASN* 1.3 62.3 + - - +
98A LEU* 3.6 2.6 + - - +
99A ALA* 3.1 26.0 + - - +
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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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12A VAL* 3.8 25.7 - - - +
73A SER* 5.5 3.1 - - - -
74A VAL 5.2 3.5 + - - -
92A GLN* 2.8 42.3 + - - +
93A GLU* 3.8 6.7 - - - +
95A ALA* 1.3 72.8 - - - +
97A CYS* 1.3 60.6 + - - +
99A ALA* 3.6 6.5 + - - +
100A GLN* 3.0 31.4 + - - +
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Residues in contact with CYS 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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41A TRP* 5.1 0.9 - - - -
42A CYS* 2.0 52.1 - - + -
93A GLU* 2.9 21.1 + - + +
94A ILE* 3.4 7.0 - - - +
96A ASN* 1.3 76.4 - - - +
98A LEU* 1.3 61.5 + - - +
100A GLN* 3.3 20.7 + - - +
101A THR* 3.3 14.0 - - - +
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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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9A VAL* 4.4 9.0 - - + -
13A GLY* 5.6 0.7 - - - -
14A PRO* 5.5 0.4 - - - -
15A ARG* 3.5 11.2 + - - -
20A TYR* 3.7 40.4 - - + +
39A ILE* 3.8 21.5 - - + +
42A CYS* 3.6 22.0 - - + -
43A CYS* 4.8 2.2 - - - -
94A ILE* 2.8 49.4 + - + +
95A ALA* 4.2 2.7 - - - +
97A CYS* 1.3 73.3 - - - +
99A ALA* 1.3 61.7 + - - +
101A THR* 2.7 23.1 + - - -
1130A TJM 3.8 18.4 - - + -
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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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12A VAL* 3.6 34.3 - - + +
13A GLY* 3.8 14.0 - - - -
14A PRO* 4.5 10.4 - - - +
95A ALA 3.1 19.3 + - - +
96A ASN 3.9 5.2 - - - +
97A CYS 3.3 0.4 - - - -
98A LEU* 1.3 75.4 - - - +
100A GLN* 1.3 58.9 + - + +
101A THR 3.4 3.8 + - - +
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Residues in contact with GLN 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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96A ASN* 3.0 28.8 + - - +
97A CYS* 3.3 12.6 + - - +
98A LEU 3.2 1.4 - - - -
99A ALA* 1.3 78.0 - - + +
101A THR* 1.3 60.5 + - + +
102A GLU* 5.5 1.7 - - - +
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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