Contacts of the strand formed by residues 22 - 32 (chain G) in PDB entry 3BXB
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 HIS 22 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G THR* 3.3 6.6 - - - +
19G VAL* 2.9 31.6 + - - +
20G ASN 4.3 2.9 - - - +
21G ASN* 1.3 80.9 - - - +
23G HIS* 1.3 72.0 + - - +
24G PHE* 3.6 8.2 - - - +
48G GLY* 3.0 30.5 - - - -
50G PRO 4.5 2.8 + - - -
51G LEU* 4.6 1.3 - - + -
52G PRO* 3.4 44.5 - - + +
53G PHE* 4.5 4.9 - - + -
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Residues in contact with HIS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LYS* 4.4 16.5 + - - -
16G GLU* 2.7 37.6 + - + +
17G GLY* 3.2 27.1 - - - -
18G THR* 3.9 12.5 - - + +
21G ASN 4.0 3.2 + - - -
22G HIS* 1.3 87.3 + - - +
24G PHE* 1.3 76.0 + - - +
25G LYS* 4.6 2.2 - - + -
47G GLU* 4.0 24.4 + - - +
48G GLY* 3.7 10.0 - - - -
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Residues in contact with PHE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G MET* 3.8 28.9 - - + -
16G GLU* 3.5 4.2 - - - +
17G GLY* 3.0 52.5 + - - +
18G THR 3.7 3.6 - - - -
19G VAL* 4.0 19.1 - - + -
22G HIS* 3.6 12.6 - - - +
23G HIS* 1.3 80.7 - - - +
25G LYS* 1.3 67.2 + - - +
26G CYS* 3.9 17.5 - - - -
47G GLU 3.1 10.3 - - - +
51G LEU* 3.4 28.7 - - + -
53G PHE* 4.1 10.8 - + - -
58G LEU* 3.7 25.1 - - + -
121G ILE* 3.9 17.3 - - + -
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Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G MET 3.1 11.7 - - - +
16G GLU* 3.4 35.0 - - + +
23G HIS* 4.6 1.8 - - + -
24G PHE* 1.3 79.7 - - - +
26G CYS* 1.3 66.9 + - - +
45G VAL* 3.5 6.6 - - - +
46G VAL* 3.0 34.2 + - + -
47G GLU* 2.9 49.7 + - + +
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Residues in contact with CYS 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 4.7 0.4 - - - -
14G TYR* 3.6 1.9 - - - +
15G MET* 2.7 47.6 + - + +
24G PHE* 3.9 23.3 - - - -
25G LYS* 1.3 79.7 - - - +
27G THR* 1.3 67.7 + - - +
43G ILE* 4.5 3.6 - - + -
44G LYS 3.2 12.1 - - - +
45G VAL* 4.3 16.4 - - - -
46G VAL* 4.5 2.0 - - - +
55G PHE* 4.7 5.2 - - - -
58G LEU* 5.0 1.8 - - - -
62G PHE* 4.0 27.1 - - + -
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Residues in contact with THR 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 3.2 14.6 - - - +
14G TYR* 4.1 18.8 - - + -
26G CYS* 1.3 80.1 - - - +
28G SER* 1.3 61.5 + - - +
43G ILE* 3.4 2.6 - - - +
44G LYS* 2.8 44.8 + - - +
46G VAL* 3.4 30.2 - - + +
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LYS* 3.5 4.0 - - - +
13G LEU* 2.8 43.4 + - - +
27G THR* 1.3 77.8 - - - +
29G GLU* 1.3 63.4 + - - +
41G MET* 3.0 30.2 - - - +
42G ARG 3.0 21.8 - - - -
43G ILE* 3.3 21.0 - - - +
44G LYS* 6.0 0.2 - - - -
62G PHE* 3.9 2.1 - - - -
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Residues in contact with GLU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G MET 3.2 7.4 - - - +
12G LYS* 2.6 42.6 + - + +
28G SER* 1.3 77.8 - - - +
30G GLY* 1.3 58.8 + - - +
41G MET* 4.2 3.6 - - - -
42G ARG* 2.9 44.8 + - + +
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Residues in contact with GLY 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G HIS* 3.3 6.7 + - - +
11G MET* 2.9 42.5 + - - +
29G GLU* 1.3 75.9 - - - +
31G GLU* 1.3 63.4 + - - +
40G THR 3.2 15.0 - - - -
41G MET* 4.1 1.6 - - - -
42G ARG* 3.2 13.4 - - - +
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Residues in contact with GLU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASN* 6.6 0.4 - - + -
9G MET 3.2 12.8 - - - +
10G HIS* 3.9 24.3 - - + +
11G MET* 3.9 6.5 - - - -
30G GLY* 1.3 74.4 - - - +
32G GLY* 1.3 60.9 + - - +
33G LYS* 6.2 3.6 - - - -
39G GLN* 3.8 0.2 - - - -
40G THR* 3.0 34.1 + - - +
42G ARG* 2.7 43.0 + - - -
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Residues in contact with GLY 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASN* 3.6 7.1 - - - +
9G MET 3.0 20.7 + - - -
31G GLU* 1.3 76.3 - - - +
33G LYS* 1.3 71.1 + - - +
34G PRO* 3.2 13.4 - - - +
38G THR* 3.3 13.7 - - - -
39G GLN* 3.8 3.8 - - - -
69G PHE* 3.5 9.3 - - - -
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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