Contacts of the strand formed by residues 38 - 47 (chain A) in PDB entry 2ZB8
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN 5.1 0.5 - - - +
34A ILE* 3.1 18.6 - - + +
35A ASN* 3.0 48.7 + - + +
36A GLU 3.0 4.2 - - - +
37A GLY* 1.3 79.4 - - - +
39A VAL* 1.3 63.1 + - - +
86A LYS* 3.2 20.1 + - - +
108A ILE* 3.4 24.5 + - + +
109A LEU 3.1 8.7 - - - +
110A ASP* 2.9 35.5 + - - +
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Residues in contact with VAL 39 (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 ILE* 4.3 5.2 - - - -
38A GLN* 1.3 80.1 - - - +
40A GLN* 1.3 59.9 + - - +
41A VAL* 3.8 11.7 - - + -
82A ILE* 4.5 7.6 - - + -
84A GLU 3.1 10.3 - - - +
85A SER* 3.5 26.5 - - - +
87A HIS* 4.0 15.0 - - + -
90A LEU* 4.0 13.5 - - + -
107A VAL 3.8 0.3 - - - +
108A ILE* 3.3 3.2 - - - -
109A LEU* 2.6 46.7 + - + +
111A GLY* 4.2 2.2 - - - -
114A LEU* 3.3 33.0 - - + -
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Residues in contact with GLN 40 (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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1A MET* 4.5 10.0 - - - +
30A LEU* 3.8 27.8 - - + +
31A PRO 4.7 4.2 - - - +
32A ASP 6.1 0.5 - - - -
34A ILE* 3.4 28.8 - - + +
39A VAL* 1.3 73.7 - - - +
41A VAL* 1.3 59.1 + - - +
82A ILE* 3.6 3.6 - - - +
83A GLU* 2.7 60.9 + - - +
84A GLU* 2.7 29.5 + - + +
106A LYS* 4.9 1.7 - - + +
107A VAL 3.6 9.4 - - - +
108A ILE* 4.5 8.7 - - + +
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Residues in contact with VAL 41 (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 VAL* 3.8 24.0 - - + +
40A GLN* 1.3 81.0 - - - +
42A ARG* 1.3 57.6 + - - +
43A THR 4.9 0.2 - - - +
81A ILE 3.3 9.0 - - - +
82A ILE* 4.4 6.1 - - + -
83A GLU* 4.5 3.4 - - - -
96A VAL* 4.4 11.0 - - + -
101A TRP* 3.4 29.2 - - + +
106A LYS* 3.4 7.0 - - - +
107A VAL* 3.0 49.9 + - + +
109A LEU* 4.6 3.6 - - + -
114A LEU* 4.1 13.0 - - + -
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Residues in contact with ARG 42 (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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41A VAL* 1.3 70.7 - - - +
43A THR* 1.3 60.9 + - - +
44A LEU* 3.5 4.9 + - - +
80A GLY* 3.2 5.5 - - - -
81A ILE* 2.7 62.7 + - + +
83A GLU* 2.7 40.9 + - - +
101A TRP* 4.6 0.7 - - - -
105A THR 3.9 8.5 - - - +
106A LYS* 4.5 13.0 - - + +
346A SER* 3.6 28.0 - - - +
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Residues in contact with THR 43 (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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41A VAL 3.9 0.5 + - - -
42A ARG* 1.3 71.2 - - - +
44A LEU* 1.3 61.4 + - - +
45A TYR 4.2 4.5 - - - +
46A LEU* 3.8 20.0 - - + -
101A TRP* 3.0 33.1 + - + +
104A GLN 2.7 25.2 + - - +
105A THR 2.9 17.5 + - - +
106A LYS* 4.2 0.9 + - - -
107A VAL* 4.4 2.6 - - - +
345A ILE* 3.6 34.3 - - + +
346A SER* 3.0 18.5 + - - -
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Residues in contact with LEU 44 (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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42A ARG* 4.0 9.2 - - - +
43A THR* 1.3 75.5 - - - +
45A TYR* 1.3 76.1 + - + +
79A ILE* 2.8 15.5 + - + +
80A GLY* 3.8 26.0 - - - +
81A ILE* 4.1 15.7 - - + +
95A PHE* 3.9 25.1 - - + -
126A LEU* 4.0 13.0 - - + -
344A CYS 3.7 0.5 - - - -
345A ILE* 2.7 29.7 + - - -
346A SER* 3.5 35.5 + - - +
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Residues in contact with TYR 45 (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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43A THR* 4.2 0.7 - - - +
44A LEU* 1.3 97.0 - - + +
46A LEU* 1.3 66.8 + - - +
78A GLY* 3.4 3.5 - - - -
79A ILE* 2.9 34.1 + - + +
126A LEU* 4.2 16.7 + - + -
127A SER* 3.8 34.8 - - - -
130A LEU* 3.8 17.0 - - + -
318A VAL* 5.0 4.5 - - + -
342A ILE* 3.5 24.7 - - + -
343A VAL 3.3 6.3 - - - +
344A CYS* 3.8 31.1 - - + -
345A ILE* 4.4 0.9 - - - -
346A SER 5.2 2.1 + - - -
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Residues in contact with LEU 46 (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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43A THR* 3.8 11.0 - - + -
45A TYR* 1.3 81.9 - - - +
47A SER* 1.3 61.9 + - - +
77A GLY 3.6 13.7 - - - +
78A GLY* 4.0 1.8 - - - -
101A TRP* 3.9 29.8 - - + -
103A TRP* 3.9 28.9 - - + +
130A LEU* 3.9 6.0 - - - +
322A LEU* 3.6 31.4 - - + -
325A MET* 3.6 26.7 - - + -
342A ILE* 3.8 3.1 - - - +
343A VAL* 2.9 34.4 + - - +
345A ILE* 3.9 7.9 - - + -
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Residues in contact with SER 47 (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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46A LEU* 1.3 76.1 - - - +
48A VAL* 1.3 65.5 + - - +
49A ASP* 2.5 27.8 + - - -
52A MET* 3.5 13.2 - - - +
77A GLY* 3.1 24.5 + - - +
103A TRP* 4.1 1.9 + - - -
130A LEU* 3.9 17.2 + - - +
325A MET* 4.0 7.1 - - - +
340A LYS* 2.8 28.6 + - - +
341A GLN 4.3 5.4 - - - -
342A ILE* 5.1 0.2 - - - -
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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