Contacts of the strand formed by residues 57 - 65 (chain A) in PDB entry 2OQ1
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 ARG 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.4 4.5 - - - -
54A HIS 2.9 35.8 + - - +
55A ASP* 3.8 14.8 + - + +
56A VAL* 1.3 85.2 + - - +
58A PHE* 1.3 67.0 + - - +
59A HIS* 3.4 13.7 + - + +
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Residues in contact with PHE 58 (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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23A GLU* 3.4 38.6 - - + +
26A LEU* 3.8 34.5 - - + -
27A LYS* 3.7 27.6 - - + -
31A MSE 3.4 41.1 - - + -
52A LEU 3.5 2.9 - - - +
53A VAL* 3.9 7.0 - - + -
56A VAL 5.5 0.4 - - - -
57A ARG* 1.3 77.8 - - - +
59A HIS* 1.3 69.1 + - - +
60A HIS* 3.7 20.4 + + + -
316B ASP* 4.4 2.6 - - - +
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Residues in contact with HIS 59 (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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50A LEU 3.6 1.0 - - - +
51A SER* 3.4 3.3 - - - -
52A LEU* 2.8 44.1 + - + +
54A HIS* 3.7 39.1 - + + +
55A ASP* 6.0 0.2 - - + -
57A ARG* 3.4 17.1 + - + +
58A PHE* 1.3 80.0 + - - +
60A HIS* 1.3 63.9 + - - +
61A PHE* 3.5 23.6 - + + -
97A PRO* 4.1 21.0 - - + +
316B ASP* 3.3 27.1 - - - +
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Residues in contact with HIS 60 (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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19A ARG* 3.5 43.7 + - + +
22A ALA* 4.9 0.4 - - - +
23A GLU* 3.0 35.8 + - - +
39A ARG* 3.1 28.9 + - - +
49A VAL* 4.1 1.8 - - + -
50A LEU 3.3 3.8 - - - -
51A SER* 3.1 32.1 + - - -
58A PHE* 3.7 19.1 + - + +
59A HIS* 1.3 73.6 + - - +
61A PHE* 1.3 62.1 + - - +
62A PRO* 4.1 0.9 - - - -
314B GLU 5.3 0.2 + - - -
315B PTR 3.6 10.7 - - + -
316B ASP* 2.8 37.6 + - - +
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Residues in contact with PHE 61 (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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49A VAL* 3.4 3.0 - - - +
50A LEU* 2.8 48.9 + - + +
52A LEU* 3.8 22.4 - - + -
59A HIS* 3.5 26.2 - + + -
60A HIS* 1.3 73.0 - - - +
62A PRO* 1.3 67.7 - - + +
63A ILE* 3.5 1.7 + - - +
73A ILE* 4.1 30.1 - - + -
95A GLY 5.3 0.4 - - - -
96A LEU* 3.8 23.6 - - + -
97A PRO* 3.7 22.9 - - + -
316B ASP* 3.5 32.3 - - + -
317B VAL* 3.8 18.2 - - - -
318B LEU* 4.5 3.1 - - + -
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Residues in contact with PRO 62 (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 CYS* 5.4 3.1 - - - -
43A ARG* 3.7 28.5 - - - +
48A TYR 3.6 6.5 - - - +
49A VAL* 4.3 6.1 - - + -
60A HIS 3.6 8.7 - - - +
61A PHE* 1.3 85.4 - - + +
63A ILE* 1.3 61.0 + - - +
64A GLU 4.0 0.8 + - - -
73A ILE* 3.7 21.2 - - + +
74A ALA* 4.2 9.2 + - + -
315B PTR 3.8 17.5 - - + -
316B ASP 3.7 14.6 - - - +
317B VAL* 6.0 1.8 - - + -
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Residues in contact with ILE 63 (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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38A LEU* 3.8 29.6 - - + -
41A CYS* 5.1 0.7 - - - +
44A SER* 4.6 1.7 + - - -
47A GLY* 3.2 7.1 - - - -
48A TYR* 2.7 48.8 + - + +
50A LEU* 4.0 13.0 - - + +
61A PHE 3.9 5.8 - - - +
62A PRO* 1.3 77.0 - - - +
64A GLU* 1.3 61.6 + - - +
71A TYR* 3.8 34.1 - - + -
72A ALA 3.6 6.5 - - - +
73A ILE* 4.0 14.8 - - + -
82A PRO* 6.1 2.7 - - + -
85A LEU* 3.9 31.9 - - + -
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Residues in contact with GLU 64 (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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44A SER* 5.2 13.0 - - - +
47A GLY* 4.8 1.8 - - - -
62A PRO 4.0 1.4 + - - -
63A ILE* 1.3 73.5 - - - +
65A ARG* 1.3 73.9 + - - +
66A GLN* 3.5 18.5 + - - +
71A TYR* 3.4 5.4 - - - -
72A ALA 2.9 34.5 + - - +
222A LYS* 3.8 28.8 + - - -
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Residues in contact with ARG 65 (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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45A LEU* 3.4 33.2 + - - +
46A GLY* 3.4 40.4 - - - +
47A GLY* 4.6 2.6 - - - -
63A ILE 4.1 1.0 + - - -
64A GLU* 1.3 83.7 - - - +
66A GLN* 1.3 73.6 + - - +
67A LEU 3.9 0.2 + - - -
69A GLY* 4.5 8.1 - - - -
70A THR 3.3 9.0 - - - +
71A TYR* 3.6 30.2 - - + -
152A GLU* 6.2 2.6 - - - +
153A LYS* 6.0 2.4 - - - +
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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