Contacts of the strand formed by residues 82 - 91 (chain A) in PDB entry 4ZCH
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A SER* 4.7 17.6 + - - +
76A ARG 3.5 7.4 - - - +
77A GLU* 3.6 33.4 + - - +
80A GLY 4.3 1.0 + - - -
81A ARG* 1.3 77.2 - - - +
83A GLU* 1.3 62.0 + - - +
118A SER* 5.5 3.0 + - - -
120A ILE* 6.2 1.8 - - - +
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Residues in contact with GLU 83 (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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75A SER* 3.3 4.1 - - - -
76A ARG* 2.8 81.3 + - + +
81A ARG* 3.7 24.5 + - - -
82A GLN* 1.3 78.1 - - - +
84A THR* 1.3 71.9 + - - +
85A LEU* 3.6 7.0 + - - +
501A 144 3.4 34.9 + - - -
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Residues in contact with THR 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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73A VAL* 3.8 20.3 - - + +
74A VAL 3.7 7.4 - - - +
75A SER* 4.1 4.1 - - - -
83A GLU* 1.3 72.9 - - - +
85A LEU* 1.3 60.6 + - - +
86A PHE 4.0 4.0 - - - +
87A ARG* 3.7 27.9 - - + -
283A ASP* 3.2 41.4 - - - +
501A 144 3.5 17.0 - - - -
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Residues in contact with LEU 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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57A LEU* 3.6 28.3 - - + -
74A VAL* 2.9 15.6 + - + +
76A ARG* 3.7 41.1 - - + +
83A GLU* 4.1 9.4 - - - +
84A THR* 1.3 77.0 - - - +
86A PHE* 1.4 68.0 + - + +
109A PHE* 3.5 48.8 - - + -
111A LEU* 4.1 9.6 - - + -
117A LEU* 4.1 15.5 - - + -
282A GLY 4.8 1.0 - - - +
283A ASP* 4.3 1.6 - - - +
286A PHE* 5.7 0.7 - - - -
501A 144 3.5 20.3 + - - -
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Residues in contact with PHE 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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57A LEU* 3.6 42.4 - - + -
59A SER* 3.9 11.0 - - - -
72A GLN* 4.1 2.6 - - + +
74A VAL* 2.9 53.2 + - + +
84A THR* 3.8 2.1 - - - +
85A LEU* 1.4 81.5 - - + +
87A ARG* 1.3 67.6 + - - +
88A CYS* 5.9 0.2 - - + -
105A SER* 3.4 45.3 - - - +
106A ALA* 4.0 2.7 - - - -
107A GLY 4.0 4.5 - - - -
109A PHE* 3.4 31.6 - + + -
283A ASP 3.2 13.7 - - - +
286A PHE* 4.1 17.0 - - + -
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Residues in contact with ARG 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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72A GLN 3.3 7.4 - - - +
73A VAL* 3.8 27.1 - - + -
84A THR* 3.7 17.3 - - + -
86A PHE* 1.3 83.3 - - - +
88A CYS* 1.3 60.2 + - - +
89A ILE* 3.4 34.6 - - + +
105A SER* 4.1 2.3 + - - -
206A GLN* 3.0 26.2 + - - +
208A LEU* 5.1 4.4 - - - +
279A SER* 5.3 0.8 + - - -
281A ASP* 2.7 26.5 + - - +
283A ASP* 3.0 21.6 + - + +
284A VAL* 3.9 22.8 - - + +
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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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71A GLY* 2.7 33.4 - - - -
72A GLN* 3.2 27.5 + - - +
86A PHE* 5.9 0.2 - - + -
87A ARG* 1.3 75.9 - - - +
89A ILE* 1.3 56.1 + - - +
90A ARG* 4.2 3.8 - - - -
103A CYS* 2.0 55.4 - - - -
104A TYR 3.5 14.4 - - - -
105A SER* 4.2 9.2 - - - -
206A GLN* 4.8 0.7 - - - -
252A SER* 3.6 12.3 - - - -
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Residues in contact with ILE 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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69A THR* 4.9 3.8 - - - -
70A MET 3.4 11.0 - - - +
71A GLY* 4.7 4.0 - - - -
72A GLN 6.3 0.2 - - - -
73A VAL* 6.4 0.4 - - + -
87A ARG* 3.4 35.9 - - + +
88A CYS* 1.3 80.5 - - - +
90A ARG* 1.3 85.3 + - - +
103A CYS* 3.9 0.2 - - - -
208A LEU* 3.8 28.3 - - + -
250A ASN* 3.5 46.7 - - + +
251A ASN* 3.9 0.4 - - - -
252A SER* 2.9 17.7 + - - -
284A VAL* 4.2 6.7 - - + -
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Residues in contact with ARG 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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63A PHE* 5.0 2.0 - - + -
69A THR* 3.4 2.9 - - - -
70A MET* 2.9 41.1 + - + +
88A CYS* 4.2 2.0 - - - -
89A ILE* 1.3 99.3 + - - +
91A SER* 1.3 63.1 + - - +
92A MET* 3.5 15.1 + - - -
101A ASN* 4.3 22.5 + - + +
102A SER 3.2 25.7 + - - +
103A CYS* 3.6 29.5 - - + +
104A TYR* 4.6 6.9 + - - +
242A GLN* 3.9 23.3 + - - +
250A ASN 3.8 3.4 - - - -
251A ASN* 3.7 11.2 + - - -
252A SER* 2.9 26.3 + - - +
253A CYS* 5.6 0.8 - - - +
254A TYR* 5.6 2.6 - - - +
393A GLN* 5.8 6.0 + - - +
403A SER 5.6 0.8 + - - -
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Residues in contact with SER 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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69A THR* 3.3 18.4 - - - +
90A ARG* 1.3 71.8 - - - +
92A MET* 1.4 65.1 + - - +
93A PRO* 4.0 1.7 - - - +
101A ASN* 4.7 6.8 + - - +
245A PRO* 3.7 27.6 - - - +
247A THR 5.2 0.2 + - - -
248A LEU 3.9 1.4 + - - -
250A ASN 2.8 31.2 + - - -
251A ASN* 3.3 18.6 + - - +
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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