Contacts of the helix formed by residues 68 - 82 (chain A) in PDB entry 1XGW
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 GLN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.5 36.6 - - + +
39A LYS* 5.9 0.6 - - - +
61A LYS* 5.6 1.2 - - - +
62A ALA* 3.7 23.1 - - + +
65A MET* 3.3 26.1 - - + +
67A GLU* 1.3 94.9 - - - +
69A PHE* 1.3 64.3 + - - +
70A PRO* 3.4 3.6 - - - -
71A GLU* 3.5 12.0 + - - +
72A LEU* 3.0 24.7 + - - +
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Residues in contact with PHE 69 (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 ALA 4.8 0.2 - - - -
63A THR* 3.6 35.7 - - + +
65A MET 3.1 9.2 + - - +
66A TYR* 3.5 8.0 + - - +
68A GLN* 1.3 78.1 - - - +
70A PRO* 1.3 71.5 - - + +
72A LEU* 3.4 7.3 - - + +
73A MET* 2.9 70.8 + - + +
108A ARG* 3.5 59.9 - - + +
109A VAL* 3.8 12.3 - - + -
112A SER* 4.4 3.6 - - - -
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Residues in contact with PRO 70 (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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66A TYR 3.5 15.5 - - - +
67A GLU 4.5 2.7 - - - +
68A GLN* 3.5 4.5 - - - -
69A PHE* 1.3 101.5 - - + +
71A GLU* 1.3 58.6 + - - +
73A MET* 3.8 2.4 - - + -
74A ASN* 2.8 44.7 + - - +
108A ARG* 5.1 6.3 - - - +
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Residues in contact with GLU 71 (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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34A SER* 2.7 31.9 + - - -
36A ILE* 3.9 14.1 - - + -
37A GLU* 3.7 24.5 - - + +
67A GLU 4.1 14.9 - - - +
68A GLN* 3.5 11.7 + - - +
69A PHE 3.4 0.2 - - - -
70A PRO* 1.3 77.0 - - - +
72A LEU* 1.3 63.4 + - - +
74A ASN* 4.5 4.5 - - - -
75A MET* 3.1 30.0 + - - +
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Residues in contact with LEU 72 (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 ILE* 3.6 38.4 - - + -
40A VAL* 3.8 15.6 - - + +
59A ILE* 3.6 24.5 - - + +
62A ALA* 3.8 8.3 - - + +
63A THR* 3.7 36.3 - - + +
68A GLN 3.0 18.6 + - - +
69A PHE* 3.4 4.7 - - - +
71A GLU* 1.3 76.2 - - - +
73A MET* 1.3 85.5 + - + +
75A MET* 3.4 1.3 + - - -
76A LEU* 3.1 20.8 + - + +
101A LEU* 4.3 4.5 - - + -
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 4.3 1.3 - - + -
69A PHE* 2.9 53.2 + - + +
70A PRO* 3.8 3.6 - - + +
72A LEU* 1.3 97.3 - - + +
74A ASN* 1.3 60.2 + - - +
76A LEU* 3.1 20.7 + - + +
77A TRP* 3.0 40.9 + - + +
98A LEU* 4.9 4.5 - - - -
101A LEU* 4.5 7.6 - - + -
109A VAL* 3.8 24.2 - - + -
112A SER* 3.4 29.8 - - - +
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Residues in contact with ASN 74 (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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70A PRO* 2.8 36.1 + - - +
71A GLU* 4.3 4.7 - - - +
73A MET* 1.3 74.5 - - - +
75A MET* 1.3 61.1 + - - +
77A TRP* 4.1 17.1 - - - +
78A SER* 3.1 26.3 + - - -
116A HIS* 6.2 1.8 - - - -
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Residues in contact with MET 75 (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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33A TYR* 3.8 39.5 - - + -
37A GLU* 3.6 34.8 - - + +
40A VAL* 3.8 13.5 - - + -
41A ARG* 3.6 30.1 - - + -
71A GLU 3.1 19.8 + - - +
72A LEU 3.9 3.6 - - - +
74A ASN* 1.3 73.3 - - - +
76A LEU* 1.3 65.0 + - - +
78A SER* 3.4 10.0 + - - -
79A ARG* 3.0 41.0 + - + +
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Residues in contact with LEU 76 (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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40A VAL* 3.6 9.7 - - + +
44A THR* 4.6 4.3 - - + -
72A LEU* 3.1 13.9 + - + +
73A MET* 3.1 21.6 + - + +
75A MET* 1.3 77.4 - - - +
77A TRP* 1.3 66.0 + - + +
79A ARG* 3.4 1.7 + - - +
80A MET* 3.0 26.7 + - + +
94A SER* 3.7 35.7 - - - +
97A LEU* 4.1 19.7 - - + -
98A LEU* 4.1 30.5 - - + +
101A LEU* 4.0 23.3 - - + -
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Residues in contact with TRP 77 (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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73A MET* 3.0 37.4 + - + +
74A ASN* 4.1 17.9 - - - +
75A MET 3.3 0.2 - - - -
76A LEU* 1.3 79.6 - - + +
78A SER* 1.3 58.9 + - - +
80A MET* 3.3 27.9 + - + -
81A LEU* 2.7 55.5 + - + +
98A LEU* 4.2 20.0 - - + -
112A SER* 3.1 39.8 + - - -
113A ALA* 4.0 12.6 - - + -
116A HIS* 3.9 32.5 + + + -
119A ASP* 5.1 0.7 - - + -
120A LEU* 4.1 22.2 - - + -
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Residues in contact with SER 78 (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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74A ASN 3.1 17.3 + - - -
75A MET* 3.4 15.9 + - - -
77A TRP* 1.3 77.6 - - - +
79A ARG* 1.3 63.1 + - - +
81A LEU* 5.0 0.4 - - - -
82A LYS* 2.8 49.2 + - - +
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Residues in contact with ARG 79 (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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40A VAL* 4.7 2.7 - - + -
41A ARG* 3.4 57.4 + - - +
44A THR* 3.0 43.9 + - + +
45A ASN* 4.2 6.5 - - - +
46A ASP* 5.9 0.6 + - - -
75A MET* 3.0 38.9 + - + +
76A LEU* 3.8 4.5 - - - +
78A SER* 1.3 78.6 + - - +
80A MET* 1.3 59.9 + - - +
82A LYS 4.7 1.1 - - - +
84A ASN* 4.7 3.3 - - - +
90A ARG* 3.4 56.5 - - - +
91A VAL* 4.4 5.0 - - - +
94A SER* 4.0 8.1 + - - +
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Residues in contact with MET 80 (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 LEU* 3.0 21.1 + - + +
77A TRP* 3.6 23.3 - - + +
79A ARG* 1.3 78.1 - - - +
81A LEU* 1.3 64.8 + - + +
84A ASN* 2.8 19.9 + - - -
91A VAL* 3.6 18.2 - - + +
94A SER* 3.7 39.2 + - - +
95A LEU* 4.0 12.1 - - + -
98A LEU* 4.2 14.6 - - + -
120A LEU* 3.5 28.3 - - + -
123A LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 81 (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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77A TRP* 2.7 40.0 + - + +
78A SER* 5.0 0.2 - - - -
80A MET* 1.3 91.6 - - + +
82A LYS* 1.3 61.0 + - - +
83A ASP 3.8 1.9 + - - -
84A ASN* 3.7 14.7 + - - +
119A ASP* 3.7 47.6 - - + +
122A SER* 4.1 5.4 - - - +
123A LEU* 3.9 27.6 - - + -
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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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78A SER* 2.8 40.6 + - - +
79A ARG* 4.7 2.6 - - - +
81A LEU* 1.3 73.5 - - + +
83A ASP* 1.3 77.8 + - + +
84A ASN* 3.4 3.3 + - - +
90A ARG* 4.9 3.8 + - - -
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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