Contacts of the strand formed by residues 26 - 34 (chain G) in PDB entry 1H64
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 GLU 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LYS* 3.5 21.4 + - - -
18G LEU* 3.3 28.7 - - + +
19G VAL 3.4 9.2 - - - +
20G ILE* 3.9 26.7 - - + +
21G LEU* 4.5 2.2 - - - +
24G GLY 4.4 7.8 - - - +
25G PHE* 1.3 87.4 - - - +
27G PHE* 1.3 62.0 + - - +
47G MET* 3.4 8.2 - - - +
48G ILE* 2.6 51.4 + - + +
49G GLN* 6.1 0.2 - - - -
50G ASP 5.8 2.1 + - - -
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Residues in contact with PHE 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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20F ILE* 4.9 2.0 - - + -
68F LEU* 4.4 12.6 - - + -
69F ALA* 4.7 2.7 - - + -
17G VAL 4.1 0.2 - - - +
18G LEU* 3.6 4.2 - - - +
19G VAL* 2.8 35.2 + - + +
21G LEU* 3.3 38.6 - - + -
26G GLU* 1.3 73.9 - - - +
28G ARG* 1.3 62.8 + - - +
42G LEU* 4.0 7.9 - - + -
45G ALA* 5.2 1.8 - - + -
46G GLU 3.4 5.6 - - - -
47G MET* 3.5 40.4 - - + -
48G ILE* 5.5 0.2 - - - -
57G TYR* 3.6 29.8 - + - -
60G ILE* 3.7 21.8 - - + -
62G ILE* 3.5 35.9 - - + -
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Residues in contact with ARG 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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55A LYS* 4.5 12.9 - - - +
16G ASP* 4.6 9.2 - - - +
17G VAL 3.4 11.7 - - - +
18G LEU* 3.2 38.9 - - + +
27G PHE* 1.3 72.0 - - - +
29G GLY* 1.3 58.0 + - - +
42G LEU* 4.3 4.3 - - - -
44G ASP 4.0 0.3 - - - +
45G ALA* 3.1 4.2 - - - +
46G GLU* 2.8 53.6 + - + +
48G ILE* 3.5 23.9 - - + +
73G THR* 4.3 16.3 - - - +
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Residues in contact with GLY 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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16G ASP* 3.2 11.6 + - - +
17G VAL* 2.9 33.1 + - - +
28G ARG* 1.3 76.2 - - - +
30G ARG* 1.3 63.2 + - - -
31G LEU 3.6 0.7 + - - -
42G LEU* 4.1 9.3 - - - +
43G ALA 3.8 2.5 - - - -
44G ASP 3.7 14.1 - - - -
45G ALA* 4.1 5.2 - - - -
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Residues in contact with ARG 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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14G ASP* 3.7 42.5 + - - +
15G LYS 3.6 6.7 - - - +
16G ASP* 4.4 1.8 - - + +
29G GLY* 1.3 71.9 - - - -
31G LEU* 1.3 65.9 + - - +
32G ILE* 3.3 28.3 + - - +
42G LEU* 3.3 2.6 - - - -
43G ALA* 2.9 52.5 + - - +
44G ASP* 2.5 31.6 + - + -
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Residues in contact with LEU 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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9G ILE* 3.4 40.8 - - + +
12G SER* 3.7 25.4 - - - +
13G LEU* 3.6 8.4 - - + +
14G ASP* 2.6 34.8 + - - -
15G LYS 2.9 11.2 + - - +
17G VAL* 4.2 14.1 - - + -
29G GLY 3.6 3.2 + - - -
30G ARG* 1.3 70.2 - - - +
32G ILE* 1.3 57.9 + - - +
33G GLY 3.4 26.2 - - - +
34G TYR* 4.7 0.7 - - + -
40G VAL* 3.9 21.3 - - + -
41G VAL 3.6 9.0 - - - +
42G LEU* 4.0 9.4 - - + +
70G ILE* 6.3 2.7 - - + -
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Residues in contact with ILE 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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3F GLU* 2.7 44.2 + - + +
13G LEU* 3.8 11.2 - - - +
14G ASP* 4.6 9.6 - - - +
30G ARG* 3.3 39.0 - - + +
31G LEU* 1.3 80.0 - - - +
33G GLY* 1.3 53.5 + - - +
41G VAL* 3.0 25.5 + - + +
43G ALA* 3.9 10.8 - - + +
59G LYS* 3.3 42.8 - - + +
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Residues in contact with GLY 33 (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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3F GLU 3.3 20.6 - - - -
4F ARG* 4.6 0.9 - - - -
13G LEU* 3.8 9.1 - - - +
31G LEU* 3.4 10.2 - - - +
32G ILE* 1.3 81.3 - - - +
34G TYR* 1.3 67.2 + - - +
40G VAL* 3.6 0.2 - - - -
41G VAL* 2.9 26.8 + - - -
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Residues in contact with TYR 34 (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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4F ARG* 3.0 45.4 + - - +
5F PRO* 3.8 10.3 - - - +
6G LEU* 3.8 23.8 + - + +
9G ILE* 3.5 27.4 - - + -
10G HIS* 3.2 47.1 + - + +
13G LEU* 4.1 24.9 - - + -
31G LEU* 4.7 1.3 - - + -
33G GLY* 1.3 79.0 - - - +
35G ASP* 1.3 72.8 - - - +
36G ILE 5.3 0.2 - - - -
38G LEU* 5.6 1.3 - - + -
39G ASN 3.2 15.7 - - - +
40G VAL* 4.0 7.0 - - + -
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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