Contacts of the strand formed by residues 89 - 105 (chain A) in PDB entry 2XAC
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.8 2.7 - - - +
82A MET* 2.8 55.8 + - + +
84A ARG* 3.4 30.7 - - - +
87A SER 3.9 2.0 + - - +
88A SER* 1.3 77.0 - - - +
90A LEU* 1.3 70.3 + - - +
91A GLY* 5.3 0.2 - - - -
142X ILE* 3.9 8.3 - - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLN* 4.2 24.5 - - + +
80A ILE 3.5 9.4 - - - +
81A LEU* 3.8 17.3 - - + -
82A MET* 3.7 2.0 - - - -
89A GLN* 1.3 87.9 + - - +
91A GLY* 1.3 58.3 + - - +
17B TRP* 3.6 34.8 - - + -
141X GLU* 3.8 36.3 - - + +
142X ILE* 3.5 20.3 - - + +
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Residues in contact with GLY 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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39A LEU* 4.5 5.4 - - - -
79A GLN* 3.1 4.5 - - - -
80A ILE* 2.7 42.4 + - - +
82A MET* 3.5 24.0 - - - +
90A LEU* 1.3 74.6 - - - +
92A GLU* 1.3 58.9 + - - -
93A MET 3.7 0.2 + - - -
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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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39A LEU* 3.4 17.8 - - - +
77A ARG* 3.4 57.0 + - + +
78A MET 4.0 2.5 - - - +
79A GLN* 4.3 4.5 - - + +
91A GLY* 1.3 70.7 - - - -
93A MET* 1.3 60.1 + - - +
94A SER* 4.1 4.0 + - - +
14B VAL* 3.5 28.0 - - + +
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Residues in contact with MET 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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35A LEU* 3.7 22.9 - - + -
36A THR* 2.9 47.6 - - + +
39A LEU* 3.6 21.1 - - + -
52A VAL* 3.6 43.1 - - + -
76A VAL 3.1 3.5 - - - +
77A ARG* 3.4 0.6 - - - -
78A MET* 2.7 50.3 + - + +
80A ILE* 3.6 11.9 - - + -
91A GLY 3.7 0.8 + - - -
92A GLU* 1.3 71.4 - - - +
94A SER* 1.3 67.2 + - - +
95A LEU* 4.4 4.3 - - + -
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Residues in contact with SER 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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36A THR* 4.1 12.5 + - - +
39A LEU* 5.2 0.8 - - - +
75A GLN* 4.1 17.0 + - - -
76A VAL 3.1 6.5 - - - -
77A ARG* 3.4 28.8 - - - +
92A GLU* 4.1 5.1 + - - +
93A MET* 1.3 74.7 - - - +
95A LEU* 1.3 63.5 + - - +
11B GLN* 4.6 3.2 + - - -
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Residues in contact with LEU 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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33A VAL* 4.0 16.8 - - + -
34A PRO 5.1 0.2 - - - +
36A THR* 3.9 22.2 - - + -
52A VAL* 3.7 19.5 - - + -
54A VAL* 3.7 26.5 - - + -
56A ARG* 4.5 5.8 - - - +
75A GLN* 3.0 34.6 - - - +
76A VAL* 3.1 37.4 + - + +
78A MET* 4.3 14.1 - - + -
93A MET* 4.4 5.8 - - + -
94A SER* 1.3 76.5 - - - +
96A GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 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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54A VAL* 4.1 4.3 - - - +
56A ARG* 2.7 44.9 + - - +
73A GLN* 2.9 33.4 + - - +
75A GLN* 3.0 14.6 + - - +
95A LEU* 1.3 74.8 - - - +
97A GLU* 1.3 57.2 + - - +
98A HIS* 3.4 28.4 + - - +
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Residues in contact with GLU 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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53A THR 5.0 1.2 - - - +
54A VAL* 3.9 7.5 - - + -
55A GLN* 3.1 50.7 + - + +
73A GLN* 3.2 1.4 - - - +
74A HIS* 2.7 77.2 + - - +
76A VAL* 3.3 37.2 - - + +
78A MET* 5.7 1.6 - - - +
96A GLU* 1.3 73.1 - - - +
98A HIS* 1.3 63.7 + - - +
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Residues in contact with HIS 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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28A PRO* 3.6 4.7 - - - +
55A GLN* 2.7 46.5 + - - +
56A ARG* 3.6 22.1 - - + -
57A CYS* 3.4 28.1 + - + -
70A PRO* 3.4 38.8 - - + +
72A GLY 3.5 3.6 - - - +
73A GLN* 3.7 15.4 + - + -
74A HIS* 4.6 1.8 - - - -
96A GLU* 3.4 33.2 + - + +
97A GLU* 1.3 79.4 - - - +
99A SER* 1.3 54.6 + - - +
101A CYS* 4.5 1.3 - - - -
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Residues in contact with SER 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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28A PRO* 3.0 27.6 - - - +
55A GLN* 3.8 7.0 - - - -
72A GLY* 2.7 23.6 + - - -
73A GLN* 3.5 5.1 + - - +
74A HIS* 3.9 17.7 + - - -
97A GLU 4.1 0.2 + - - -
98A HIS* 1.3 73.2 - - - +
100A GLN* 1.3 78.5 + - - +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 3.3 4.3 - - - +
71A THR* 2.7 40.8 + - - +
72A GLY* 2.9 25.4 + - - +
99A SER* 1.3 91.0 + - - +
101A CYS* 1.3 59.3 + - - +
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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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26A CYS* 4.1 10.1 - - - +
27A GLN* 4.1 16.4 - - - -
28A PRO* 3.4 28.4 - - + +
57A CYS* 2.0 54.5 - - + -
69A VAL 3.3 4.5 - - - +
71A THR* 3.7 5.8 + - - -
98A HIS* 4.5 2.0 - - - -
99A SER 4.0 0.6 + - - -
100A GLN* 1.3 79.2 - - - +
102A GLU* 1.3 66.3 + - - +
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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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26A CYS* 3.7 6.7 - - - -
69A VAL* 2.6 45.4 + - - +
71A THR* 3.4 31.7 + - + +
101A CYS* 1.3 79.0 - - - +
103A CYS* 1.3 60.9 + - - +
104A ARG* 3.6 24.8 + - + -
199C TYR* 5.2 2.3 + - + -
200C LYS* 4.6 23.0 - - + -
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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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25A THR* 5.9 1.6 - - - -
26A CYS* 3.3 28.9 - - + +
60A CYS 4.2 0.7 - - - -
61A CYS* 2.0 57.4 - - + -
62A PRO* 4.4 5.2 - - + -
66A LEU* 4.5 10.9 - - + +
67A GLU 3.6 0.9 - - - -
102A GLU* 1.3 74.0 - - - +
104A ARG* 1.3 60.4 + - - +
199C TYR* 3.6 21.3 - - - -
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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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66A LEU* 3.7 4.9 - - - -
67A GLU* 2.5 44.3 + - + +
69A VAL* 3.7 27.2 - - + +
71A THR* 5.3 4.8 - - - +
102A GLU* 3.4 29.1 + - + +
103A CYS* 1.3 79.0 - - - +
105A PRO* 1.4 73.0 - - + +
199C TYR* 4.2 18.1 + - + -
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Residues in contact with PRO 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 GLY 4.0 3.1 - - - +
66A LEU* 3.5 17.0 - - + -
67A GLU* 4.4 4.9 - - - +
104A ARG* 1.4 96.5 - - + +
106A LYS* 1.3 67.5 + - - +
107A LYS* 5.4 0.5 - - - +
150C GLU* 5.3 2.9 - - - +
199C TYR* 3.6 36.1 - - + -
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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
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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