Contacts of the strand formed by residues 3 - 13 (chain G) in PDB entry 3HOX
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 PHE 3 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LEU* 4.6 4.7 - - + -
33D PHE* 3.6 31.9 - + + -
47D LEU* 3.2 34.8 - - + -
48D ILE 3.3 7.2 - - - +
49D ALA* 4.4 5.6 - - + -
50D LEU* 4.9 0.4 - - - +
173D HIS* 6.2 0.9 - + - -
175D PHE* 4.4 15.7 - + + -
1G MET* 3.0 52.5 - - + -
2G PHE* 1.3 74.3 - - - +
4G ILE* 1.3 68.3 + - - +
5G LYS* 4.8 0.9 - - + +
77G VAL* 3.3 7.1 - - - +
78G VAL* 2.7 51.9 + - + +
80G LYS* 4.0 11.4 - - + -
82G PHE* 3.7 23.8 - + - -
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Residues in contact with ILE 4 (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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37D GLN* 4.9 4.0 + - - -
47D LEU* 5.9 0.2 - - - +
48D ILE* 3.2 42.0 + - + +
50D LEU* 3.2 45.5 - - + -
58D VAL* 4.7 11.0 - - + -
3G PHE* 1.3 79.0 - - - +
5G LYS* 1.3 58.1 + - - +
49G LEU* 4.2 7.6 - - + -
75G ARG* 3.5 38.1 + - + +
76G ALA 3.2 11.9 - - - +
77G VAL* 3.9 10.1 - - + -
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Residues in contact with LYS 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 3.3 15.7 - - - -
8D PHE* 3.0 36.9 - - + -
9D GLN* 4.9 1.0 - - - -
32D GLU* 2.6 55.3 + - - +
33D PHE* 4.6 9.9 - - + -
37D GLN* 3.2 13.5 + - - +
3G PHE* 4.0 1.9 - - + -
4G ILE* 1.3 75.4 - - - +
6G ASP* 1.3 63.2 + - - +
7G LEU* 3.4 25.6 + - + +
42G PHE* 4.5 4.5 - - + -
75G ARG* 3.7 3.1 - - - +
76G ALA* 3.1 30.1 + - - +
78G VAL* 4.2 19.8 - - + +
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Residues in contact with ASP 6 (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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8D PHE* 2.8 49.5 + - + +
37D GLN* 4.8 4.2 + - - +
38D ILE 3.9 2.5 - - - +
39D ASN* 3.2 28.8 - - - +
40D HIS* 4.2 24.0 + - + +
45D GLU* 4.1 5.5 - - - +
4G ILE 5.9 0.2 - - - -
5G LYS* 1.3 71.4 - - - +
7G LEU* 1.3 66.5 + - - +
74G TYR 4.0 3.1 - - - -
75G ARG* 2.8 40.8 + - - +
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Residues in contact with LEU 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 4.0 6.7 - - - +
6D SER 3.6 15.7 - - - +
7D THR* 3.9 3.6 - - - +
40D HIS* 2.7 32.7 - - - -
5G LYS* 3.4 28.9 + - + +
6G ASP* 1.3 79.9 - - - +
8G SER* 1.3 61.1 - - - +
42G PHE* 3.7 26.0 - - + -
45G ILE* 3.2 36.1 - - + -
74G TYR* 2.9 39.3 + - + +
75G ARG* 5.7 0.7 - - - -
76G ALA* 5.8 3.8 - - + +
78G VAL* 4.8 6.5 - - + -
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Residues in contact with SER 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 3.2 10.2 + - - -
6D SER* 2.8 49.3 + - - -
7D THR* 4.8 0.9 - - - -
8D PHE 5.8 0.9 - - - -
40D HIS* 4.5 7.4 - - - -
7G LEU* 1.3 80.3 - - - +
9G LEU* 1.3 63.6 + - - +
10G ASN* 5.5 0.5 + - - -
71G ASN* 2.9 23.3 + - - -
72G VAL 3.4 10.8 - - - -
73G LYS* 4.6 5.8 - - - -
74G TYR* 3.7 3.8 - - - -
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Residues in contact with LEU 9 (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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3D VAL* 4.1 12.3 - - - +
4D SER 3.9 29.2 - - - +
5D THR* 4.1 3.4 - - - +
6D SER* 4.9 0.7 - - - +
8G SER* 1.3 77.3 + - - +
10G ASN* 1.3 82.1 + - - +
11G ILE* 4.1 9.0 - - + -
30G LEU* 3.8 27.4 - - + +
33G GLU* 4.3 23.8 - - + +
34G VAL* 3.4 30.5 - - + -
70G PHE 3.8 0.2 - - - +
71G ASN* 3.6 2.6 - - - +
72G VAL* 2.8 34.3 + - + +
74G TYR* 4.9 0.7 - - + -
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Residues in contact with ASN 10 (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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12A ARG* 6.0 2.0 - - - +
3D VAL* 3.9 30.6 + - - +
6D SER* 6.0 4.0 - - - -
8G SER* 5.5 0.6 + - - -
9G LEU* 1.3 84.3 - - - +
11G ILE* 1.3 65.9 + - - +
12G THR 4.2 0.7 + - - -
33G GLU* 5.3 2.3 - - - +
69G GLU* 4.0 24.9 + - - +
70G PHE 3.5 3.8 - - - +
71G ASN* 3.4 32.6 + - - +
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Residues in contact with ILE 11 (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 LEU* 4.3 13.0 - - + -
10G ASN* 1.3 80.4 - - - +
12G THR* 1.3 71.1 + - - +
13G LEU* 3.7 1.4 + - + -
26G LEU* 4.1 27.6 - - + +
29G LYS* 4.3 23.1 - - + -
30G LEU* 4.0 35.2 - - + +
33G GLU* 5.6 5.2 - - - +
68G ALA 3.6 1.7 - - - +
69G GLU* 3.2 4.2 - - - +
70G PHE* 2.8 42.6 + - + +
72G VAL* 4.2 22.9 - - + -
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Residues in contact with THR 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 6.1 1.2 - - - +
3D VAL* 6.4 1.8 - - - +
10G ASN 4.2 1.2 + - - -
11G ILE* 1.3 78.6 - - - +
13G LEU* 1.3 61.1 + - - +
14G HIS 3.9 1.6 + - - -
62G LEU* 5.6 6.0 - - + +
67G SER* 3.6 26.2 - - - +
68G ALA 3.5 4.0 - - - +
69G GLU* 3.8 24.4 + - - +
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 3.7 2.3 + - + -
12G THR* 1.3 73.9 - - - +
14G HIS* 1.3 69.8 + - - +
17G PHE* 3.1 49.8 - - + -
18G PHE* 3.7 3.3 - - + -
22G MET* 3.5 39.7 - - + -
25G TYR* 4.5 12.3 - - + -
26G LEU* 4.1 19.5 - - + -
67G SER* 2.9 26.6 - - - -
68G ALA 2.8 20.0 + - - +
70G PHE* 3.9 20.0 - - + -
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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