Contacts of the strand formed by residues 8 - 16 (chain H) in PDB entry 4FAO
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 CYS 8 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H HIS* 1.3 81.1 - - - +
9H GLN* 1.3 65.3 + - - +
38H LYS 3.4 4.0 - - - -
39H GLY* 3.9 0.4 - - - -
40H GLY 3.3 19.3 + - - +
41H CYS* 4.9 0.2 - - - -
49H VAL* 4.4 23.4 - - + +
74H CYS* 2.0 46.2 - - + -
107H CYS* 4.7 2.2 - - - -
108H GLY 4.3 12.1 - - - -
109H CYS* 4.4 12.1 - - - -
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Residues in contact with GLN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H SER* 3.2 29.5 - - - +
7H HIS 4.5 3.5 - - - +
8H CYS* 1.3 83.3 - - - +
10H LYS* 1.3 68.1 + - - +
11H THR* 4.2 6.8 + - - +
37H CYS* 3.7 3.8 - - - -
38H LYS* 2.9 38.7 + - + +
107H CYS* 3.7 10.2 - - - -
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Residues in contact with LYS 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLN* 1.3 83.1 - - - +
11H THR* 1.3 62.2 + - - +
35H TYR* 3.4 57.4 + - + -
36H GLU 3.6 2.7 - - - +
104H VAL* 4.0 18.2 + - + +
105H ALA* 3.2 27.3 + - - +
106H GLU* 5.1 1.3 - - - +
107H CYS* 3.7 12.7 - - + +
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Residues in contact with THR 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLN* 4.2 6.8 + - - +
10H LYS* 1.3 75.5 + - - +
12H SER* 1.3 76.8 + - - +
35H TYR* 3.1 14.7 - - - -
36H GLU* 2.9 42.2 + - + -
38H LYS* 3.8 43.6 - - + +
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Residues in contact with SER 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H THR* 1.3 89.7 - - - +
13H LEU* 1.3 62.0 + - - +
14H ARG* 3.8 16.6 + - - +
33H GLU* 2.9 26.3 + - - -
35H TYR* 4.0 4.0 - - - -
36H GLU* 4.7 1.4 - - - +
38H LYS* 5.1 0.9 + - - -
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Residues in contact with LEU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G HIS* 5.0 0.4 - - - +
57G VAL* 6.0 0.2 - - + -
58G GLN* 4.7 25.1 - - + +
61G VAL* 4.3 9.9 - - + -
69G VAL* 3.6 30.3 - - + -
11H THR 3.5 0.2 + - - -
12H SER* 1.3 74.4 + - - +
14H ARG* 1.3 64.6 + - - +
15H VAL* 3.1 21.3 + - + -
33H GLU* 2.6 11.3 + - - -
34H ALA* 2.5 41.1 + - + +
35H TYR 3.6 22.2 - - - +
36H GLU* 4.0 17.0 - - + +
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G VAL* 6.0 0.9 - - - +
12H SER* 3.8 9.7 + - - +
13H LEU* 1.3 75.4 - - - +
15H VAL* 1.3 62.4 + - - +
16H ASN* 3.7 3.3 + - - +
31H GLU* 4.0 21.5 + - - +
32H TYR 3.6 2.2 - - - +
33H GLU* 3.2 29.6 + - - +
64L PHE* 3.1 61.3 - - - +
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Residues in contact with VAL 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G VAL* 3.7 33.9 - - + -
61G VAL* 3.8 23.6 - - + -
13H LEU* 3.1 20.8 + - + +
14H ARG* 1.3 72.5 - - - +
16H ASN* 1.3 72.1 + - - +
17H PHE* 3.9 2.6 + - + +
19H ASP* 6.2 0.2 - - + -
20H ILE* 4.3 12.1 - - + -
31H GLU* 3.1 3.4 - - - +
32H TYR* 2.9 51.1 + - + -
34H ALA* 4.0 13.5 - - + -
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Residues in contact with ASN 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G VAL* 5.8 0.2 - - - +
14H ARG 3.7 4.4 + - - +
15H VAL* 1.3 80.3 - - - +
17H PHE* 1.3 58.8 + - - +
18H GLU* 2.9 33.3 + - - +
19H ASP* 2.8 51.8 + - - +
20H ILE 3.6 2.4 + - - -
30H LYS* 3.4 10.9 - - - +
31H GLU* 3.6 25.2 + - - +
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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