Contacts of the strand formed by residues 116 - 132 (chain A) in PDB entry 2QCW
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 VAL 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.8 23.1 - - + -
108A LEU* 3.9 18.6 - - + -
109A TYR 3.7 2.7 - - - -
110A PHE* 3.7 22.7 - - + -
114A SER 4.2 3.6 - - - +
115A ASN* 1.3 70.7 - - - +
117A ILE* 1.3 63.6 + - - +
118A LEU 4.4 0.5 + - - -
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Residues in contact with ILE 117 (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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107A VAL 3.5 1.9 - - - +
108A LEU* 3.3 7.4 - - - -
109A TYR* 3.0 66.4 + - + +
111A ASP* 3.8 20.0 - - - +
115A ASN* 3.8 24.9 - - + +
116A VAL* 1.3 77.1 - - - +
118A LEU* 1.3 70.2 + - - +
119A LYS* 4.5 5.8 - - + -
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Residues in contact with LEU 118 (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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106A SER* 4.1 20.4 - - - +
107A VAL 3.6 17.3 - - - +
108A LEU* 3.8 21.3 - - + +
116A VAL 4.4 0.6 + - - -
117A ILE* 1.3 78.7 - - - +
119A LYS* 1.3 69.5 + - - +
120A LYS 5.2 0.4 - - - +
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Residues in contact with LYS 119 (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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106A SER* 4.3 2.2 - - - -
107A VAL 2.9 34.0 + - - +
109A TYR* 4.1 20.6 + - + +
117A ILE* 4.5 4.9 - - + -
118A LEU* 1.3 78.4 - - - +
120A LYS* 1.3 73.5 + - - +
121A TYR* 3.3 51.6 + - + +
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Residues in contact with LYS 120 (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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104A ALA* 3.8 28.2 - - + +
105A ILE 3.5 5.1 - - - +
106A SER* 2.7 37.4 + - - +
118A LEU* 5.2 1.4 - - - +
119A LYS* 1.3 80.1 - - - +
121A TYR* 1.3 61.5 + - - +
122A ARG* 4.0 22.3 + - + +
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Residues in contact with TYR 121 (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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104A ALA* 3.1 3.7 - - - -
105A ILE 2.6 37.2 + - - +
107A VAL* 4.3 23.1 - - + -
109A TYR* 4.2 14.5 + + - -
119A LYS* 3.3 70.5 + - + +
120A LYS* 1.3 72.5 - - - +
122A ARG* 1.3 62.0 + - - +
124A MET* 3.1 32.4 - - + +
76B ASN* 4.2 19.7 - - - +
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Residues in contact with ARG 122 (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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104A ALA* 4.0 14.8 - - + -
120A LYS* 4.0 20.0 + - + +
121A TYR* 1.3 75.9 - - - +
123A ASN* 1.3 81.6 + - - +
124A MET 3.3 0.5 + - - -
76B ASN* 2.6 34.4 + - - +
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Residues in contact with ASN 123 (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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102A LEU* 3.7 37.5 - - + +
103A ASN 3.5 7.1 + - - -
122A ARG* 1.3 84.1 - - - +
124A MET* 1.3 54.5 + - - +
125A VAL 3.9 0.7 - - - -
70B ALA 5.7 3.2 + - - -
75B THR* 3.9 31.0 - - - +
76B ASN* 3.4 4.1 - - - +
77B HIS* 2.7 35.0 + - - +
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Residues in contact with MET 124 (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 PHE* 5.3 5.6 - - + -
45A TRP* 6.3 1.3 - - + -
55A TYR* 3.5 41.0 + - + +
57A ALA 4.0 0.5 - - - +
103A ASN 2.7 14.3 + - - +
105A ILE* 3.5 40.2 - - + +
107A VAL* 5.4 0.9 - - + -
121A TYR* 3.1 42.6 - - + +
122A ARG 3.5 2.9 - - - +
123A ASN* 1.3 73.5 - - - +
125A VAL* 1.3 59.5 + - - +
76B ASN* 3.4 28.3 - - - -
77B HIS* 3.0 24.0 - - - -
80B VAL* 4.5 10.1 - - + -
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Residues in contact with VAL 125 (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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55A TYR* 4.1 3.6 - - + -
56A ALA* 3.5 25.4 - - + +
57A ALA 3.8 2.7 - - - -
58A ASN* 4.1 5.8 - - - +
102A LEU* 2.9 7.9 - - - -
103A ASN* 2.6 52.6 + - + +
104A ALA 4.5 0.2 - - - +
105A ILE* 3.5 30.5 - - + -
124A MET* 1.3 76.9 - - - +
126A VAL* 1.3 72.6 + - - +
127A ARG* 3.4 11.7 + - + -
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Residues in contact with VAL 126 (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 LYS* 3.7 10.7 - - + +
57A ALA 2.9 14.3 + - - +
58A ASN* 2.7 35.1 + - + +
59A TYR* 4.4 4.3 - - - -
60A CYS* 3.8 24.5 - - - -
99A PRO* 3.6 24.7 - - + -
101A LYS 3.7 4.5 - - - +
102A LEU* 4.3 3.1 - - + +
124A MET 3.9 0.4 + - - -
125A VAL* 1.3 71.4 - - - +
127A ARG* 1.3 61.2 + - - +
128A ALA 4.1 8.5 - - - +
129A CYS* 3.9 9.2 - - - -
77B HIS* 3.2 35.2 - - + +
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Residues in contact with ARG 127 (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 LYS* 3.2 30.2 + - - +
58A ASN* 5.3 1.8 - - - +
101A LYS* 2.8 34.2 + - + +
103A ASN* 2.8 47.6 + - - +
125A VAL* 3.4 9.3 + - + +
126A VAL* 1.3 77.7 - - - +
128A ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 128 (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 LYS* 4.8 2.9 - - - -
71A HIS 6.0 1.6 - - - +
99A PRO* 3.4 6.6 - - - +
100A THR* 2.7 43.5 + - - +
101A LYS* 3.4 18.1 + - + +
126A VAL* 3.7 1.4 - - - +
127A ARG* 1.3 82.0 - - - +
129A CYS* 1.3 61.7 + - - +
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Residues in contact with CYS 129 (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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31A CYS* 4.1 13.2 - - - +
32A ARG* 4.0 13.7 - - - -
33A LYS* 3.5 23.3 - - - +
60A CYS* 2.0 57.9 - - + -
71A HIS* 5.2 3.8 - - - +
72A MET* 3.9 17.5 - - - +
98A ALA 3.4 3.4 - - - +
100A THR* 3.7 4.9 + - - +
126A VAL* 3.9 5.4 - - - -
128A ALA* 1.3 77.6 - - - +
130A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 130 (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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31A CYS* 3.1 21.0 - - - -
72A MET* 4.0 13.7 - - - -
97A CYS* 3.4 0.5 - - - -
98A ALA 2.7 24.9 + - - -
100A THR* 3.1 22.0 - - - +
129A CYS* 1.3 74.3 - - - +
131A CYS* 1.3 61.2 + - - -
132A HIS* 3.7 4.7 - - - -
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Residues in contact with CYS 131 (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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31A CYS* 3.8 16.2 - - - -
64A CYS* 2.1 55.6 - - + -
68A LEU* 4.3 15.5 - - + -
72A MET* 3.8 25.0 + - - +
73A ASN 5.7 0.2 - - - -
74A ALA* 3.6 19.4 - - + +
75A THR 4.1 2.1 + - - -
78A ALA* 3.6 15.6 - - + +
95A PRO* 4.4 4.9 - - + -
96A CYS 3.7 0.2 - - - -
130A GLY* 1.3 69.3 - - - -
132A HIS* 1.3 65.8 + - - +
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Residues in contact with HIS 132 (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 ASN 6.0 2.2 - - - -
74A ALA* 6.4 0.4 - - - -
75A THR* 4.6 19.4 + - + +
77A HIS* 4.6 9.4 + - - +
78A ALA* 4.3 10.1 - - - +
81A GLN* 4.8 4.9 - - - +
95A PRO* 3.3 13.5 - - - +
96A CYS* 2.9 35.8 + - - +
98A ALA* 3.5 29.6 + - + -
99A PRO 3.4 19.8 + - - -
100A THR* 3.4 24.1 - - + +
130A GLY* 3.7 5.4 - - - -
131A CYS* 1.3 81.3 + - - +
97B CYS 5.2 0.3 - - - +
98B ALA* 3.9 19.3 - - + +
99B PRO* 3.5 32.1 + - + +
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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