Contacts of the strand formed by residues 9 - 14 (chain G) in PDB entry 5EEZ
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 9 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F ASP* 3.6 38.1 - - + -
9F PHE 5.6 2.7 - - - -
10F VAL* 5.9 0.9 - - + -
48F PHE* 4.3 13.5 - + + -
65F THR* 3.7 22.0 - - + -
66F ARG* 4.1 9.2 - - + -
67F HIS* 3.0 57.1 + + - -
7G SER 4.7 1.3 - - - -
8G ASP* 1.3 87.5 + - - +
10G VAL* 1.3 68.8 + - - +
11G VAL* 3.7 14.4 - - + -
45G ILE* 3.4 24.2 - - + -
46G ALA 3.2 20.0 - - - +
47G GLN* 3.9 9.4 - - + +
48G PHE* 4.7 0.7 - - - +
64G GLN 4.4 0.3 - - - +
65G THR* 4.5 4.2 - - - -
66G ARG 4.8 0.2 + - - -
9H PHE* 5.5 1.0 - - - -
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Residues in contact with VAL 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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9G PHE* 1.3 82.9 - - - +
11G VAL* 1.3 63.2 + - - +
12G ILE* 3.5 24.9 - - + +
44G LEU 3.7 1.0 - - - +
45G ILE* 3.4 2.4 - - - -
46G ALA* 2.8 41.6 + - + +
48G PHE* 4.3 13.2 - - + -
55G ILE* 4.1 19.7 - - + -
63G ILE* 4.8 4.3 - - + -
64G GLN 3.5 9.0 - - - +
65G THR* 4.0 17.9 - - + -
9H PHE* 5.6 1.1 - - + -
45H ILE* 4.2 24.5 - - + -
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Residues in contact with VAL 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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65F THR* 4.0 13.7 - - + +
67F HIS* 4.1 2.7 - - + -
70F ILE* 3.9 29.8 - - + -
9G PHE* 3.7 28.3 - - + -
10G VAL* 1.3 72.6 - - - +
12G ILE* 1.3 64.0 + - - +
13G LYS 4.2 0.2 - - - -
43G VAL* 3.9 14.8 - - + -
44G LEU 3.5 4.0 - - - +
45G ILE* 4.3 9.4 - - + +
62G TYR 3.8 0.3 - - - +
63G ILE* 3.2 8.8 - - - +
64G GLN* 2.9 62.8 + - - +
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Residues in contact with ILE 12 (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 VAL* 3.5 30.7 - - + +
11G VAL* 1.3 76.3 - - - +
13G LYS* 1.3 60.9 + - - +
19G VAL* 4.7 0.7 - - + -
21G VAL* 3.8 37.9 - - + -
38G LEU* 3.9 18.6 - - + +
42G GLU 3.8 1.0 - - - +
43G VAL* 3.2 5.9 - - - -
44G LEU* 2.7 51.0 + - + +
46G ALA* 4.9 2.0 - - + -
55G ILE* 5.0 0.2 - - + -
57G VAL* 4.2 17.3 - - + -
61G ALA* 3.7 25.4 - - + -
62G TYR 3.6 2.5 - - - -
63G ILE* 4.2 12.8 - - + -
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Residues in contact with LYS 13 (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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70F ILE* 4.0 24.0 - - + -
71F GLU* 2.9 27.2 + - - +
73F GLU* 2.6 38.7 + - - -
11G VAL* 4.9 0.8 - - - +
12G ILE* 1.3 74.1 - - - +
14G ALA* 1.4 71.9 + - - +
15G LEU* 3.9 15.8 - - + +
41G GLY* 4.5 9.0 - - - +
42G GLU 3.5 8.7 - - - +
43G VAL* 4.1 10.1 - - + +
61G ALA* 3.1 4.8 - - - -
62G TYR* 2.8 49.8 + - + +
28P ALA* 3.4 20.0 - - - +
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Residues in contact with ALA 14 (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 ILE 4.1 0.8 + - - -
13G LYS* 1.4 77.3 - - - +
15G LEU* 1.3 59.6 + - - +
16G GLU 3.6 12.1 - - - +
19G VAL* 3.7 10.1 - - + -
38G LEU* 3.6 24.9 - - + +
39G ASP 3.2 25.6 - - - +
40G LYS* 4.4 0.3 - - - +
41G GLY* 2.9 25.9 + - - -
42G GLU 2.9 9.6 + - - +
60G LYS 3.9 4.3 - - - -
61G ALA* 4.3 2.0 - - - -
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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