Contacts of the strand formed by residues 100 - 110 (chain A) in PDB entry 6NQN
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 ILE 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A SER* 3.5 24.0 - - - +
93A MET 3.4 4.0 - - - +
94A ASN* 3.4 44.9 - - + +
98A GLY 4.1 7.0 - - - +
99A GLY* 1.3 73.9 - - - +
101A CYS* 1.3 63.1 + - - +
102A ASN* 4.2 0.9 - - - +
122A GLY* 3.2 1.0 - - - -
123A VAL* 2.9 44.5 + - + +
124A ASN* 5.1 0.4 - - - +
125A PHE* 4.2 1.0 - - - -
92C SER* 3.3 21.8 - - - +
94C ASN* 6.1 0.9 - - - +
100C ILE* 4.6 7.4 - - + -
102C ASN* 3.2 26.7 + - - +
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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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56A ILE* 4.3 4.9 - - - -
92A SER* 3.4 2.8 - - - -
93A MET* 2.7 56.2 + - + +
95A TYR* 4.1 8.1 - - + -
100A ILE* 1.3 71.9 - - - +
102A ASN* 1.3 63.1 + - - +
120A PHE* 3.5 35.4 - - + -
121A ASP 3.4 4.5 - - - +
122A GLY* 3.7 7.0 - - - -
125A PHE* 3.4 37.5 - - - -
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Residues in contact with ASN 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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91A ARG 3.3 3.1 - - - -
92A SER* 2.8 28.9 + - - -
100A ILE* 4.2 1.6 - - - +
101A CYS* 1.3 72.9 - - - +
103A ALA* 1.3 61.9 + - - +
119A ARG* 4.0 0.5 - - - +
120A PHE* 3.6 1.7 - - - -
121A ASP* 2.8 35.0 + - - +
100C ILE* 3.3 19.8 + - - +
102C ASN* 3.4 28.2 + - + +
121C ASP* 3.3 31.2 + - + +
123C VAL* 3.6 21.4 - - + +
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Residues in contact with ALA 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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60A VAL* 3.7 36.8 - - + -
89A TRP* 3.6 7.7 - - + -
90A GLU* 3.4 2.3 - - - -
91A ARG 2.8 34.5 + - - +
93A MET* 3.9 9.9 - - + -
101A CYS 4.2 0.2 - - - -
102A ASN* 1.3 75.2 - - - +
104A THR* 1.3 65.8 + - - +
119A ARG 3.2 11.7 - - - +
120A PHE* 4.1 4.9 - - + -
123C VAL* 4.2 1.3 - - - +
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Residues in contact with THR 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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89A TRP* 3.3 12.1 - - - +
90A GLU* 4.3 9.9 - - + -
103A ALA* 1.3 79.4 - - - +
105A ASN* 1.3 61.9 + - - +
117A GLU 4.4 1.6 + - - -
118A ILE* 3.2 8.2 - - - +
119A ARG* 3.0 47.8 + - + +
17C ALA* 6.3 1.1 - - + -
20C GLY* 4.1 30.0 - - - +
122C GLY 5.4 0.2 - - - +
123C VAL* 3.8 22.0 - - + -
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Residues in contact with ASN 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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60A VAL 4.3 0.6 + - - -
63A KZ4 3.1 24.5 + - - -
88A SER* 3.2 5.9 - - - -
89A TRP* 3.0 56.9 + - + +
104A THR* 1.3 77.6 - - - +
106A ASP* 1.3 68.1 + - - +
107A ILE* 3.6 15.9 + - - +
116A TYR* 3.1 39.6 - - - +
117A GLU 3.4 3.0 + - - -
118A ILE* 3.5 17.9 - - + +
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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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87A TYR 4.2 1.1 - - - -
88A SER* 3.8 12.1 - - - -
105A ASN* 1.3 71.9 - - - +
107A ILE* 1.3 58.9 + - - +
108A THR* 3.9 11.4 + - - +
115A ILE 3.3 5.2 - - - +
117A GLU* 2.9 54.2 + - - +
180A LYS* 3.3 30.2 + - - -
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Residues in contact with ILE 107 (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 KZ4 3.7 8.1 - - - +
65A ASN* 3.6 15.5 - - + +
83A PHE* 3.9 21.5 - - + -
86A GLY* 3.6 2.4 - - - -
87A TYR* 3.0 58.6 + - + +
89A TRP* 4.1 3.4 - - - +
105A ASN* 3.6 35.9 - - - +
106A ASP* 1.3 71.5 - - - +
108A THR* 1.3 66.6 + - - +
114A TYR* 4.3 2.0 - - + -
115A ILE 3.3 2.2 - - - -
116A TYR* 3.9 20.0 - - + -
180A LYS* 2.6 25.1 + - - -
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Residues in contact with THR 108 (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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83A PHE* 4.4 4.3 - - - -
85A GLU 4.6 9.4 - - - +
106A ASP* 4.0 12.3 + - - +
107A ILE* 1.3 77.4 - - - +
109A LEU* 1.3 63.7 + - - +
114A TYR* 3.4 5.9 - - - +
115A ILE* 2.9 47.5 + - - +
180A LYS* 3.3 21.5 - - - +
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Residues in contact with LEU 109 (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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4A ILE* 5.3 9.4 - - + -
8A MET* 3.6 31.4 - - + -
83A PHE* 3.8 24.0 - - + -
84A PRO* 3.7 37.8 + - + +
108A THR* 1.3 80.8 - - - +
110A ASP* 1.3 60.2 + - - +
111A GLY 3.6 19.9 + - - +
113A CYS 3.5 19.1 - - - +
114A TYR* 3.8 8.5 - - + -
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Residues in contact with ASP 110 (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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109A LEU* 1.3 73.6 - - - +
111A GLY* 1.3 62.9 + - - +
112A ASP* 3.1 1.6 + - - +
113A CYS* 2.8 36.5 + - + +
115A ILE* 4.2 18.4 - - + +
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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