Contacts of the strand formed by residues 10 - 17 (chain M) in PDB entry 3FKS
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 THR 10 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8M PRO* 4.2 9.4 + - + +
9M ILE* 1.3 80.1 - - - +
11M GLY* 1.3 59.0 + - - +
25M PHE* 3.6 14.4 - - - +
29M GLU* 3.6 17.9 + - - +
75M LYS* 5.4 20.0 - - + -
76M VAL 3.5 7.0 - - - +
77M LEU* 5.5 5.4 - - + -
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Residues in contact with GLY 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M THR* 1.3 77.4 - - - +
12M LYS* 1.3 60.4 + - - -
23M VAL* 3.7 4.0 - - - -
24M HIS 3.7 11.9 - - - -
25M PHE* 3.7 13.9 - - - -
74M GLU 3.2 2.0 - - - +
75M LYS* 4.7 2.4 - - - +
76M VAL* 2.8 49.1 + - - +
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Residues in contact with LYS 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLY* 1.3 72.3 - - - -
13M VAL* 1.3 72.3 + - - +
14M THR* 3.7 1.8 + - - +
23M VAL* 3.9 1.8 - - - -
24M HIS* 3.0 47.7 + - + +
26M GLU* 5.3 7.9 - - - +
73M GLY* 4.7 12.6 - - - +
74M GLU 3.3 7.9 - - - +
75M LYS* 5.0 2.7 - - + +
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Residues in contact with VAL 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLY 3.8 0.2 + - - -
12M LYS* 1.3 80.3 - - - +
14M THR* 1.3 64.1 + - - +
15M ALA 3.8 5.4 - - - +
16M VAL* 3.8 18.8 - - + -
21M VAL* 3.8 26.2 - - + -
22M ASP 3.6 11.7 - - - +
23M VAL* 4.3 3.1 - - + +
39M ILE* 4.4 5.4 - - + -
70M LEU* 5.0 3.4 - - + -
71M VAL 4.5 2.0 - - - +
72M ARG* 4.3 5.9 - - - +
73M GLY* 3.4 30.3 + - - +
74M GLU* 3.1 21.6 + - + +
76M VAL* 3.6 25.8 - - + -
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Residues in contact with THR 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L PRO* 3.8 34.5 - - + +
12M LYS* 3.7 0.9 + - - +
13M VAL* 1.3 75.9 - - - +
15M ALA* 1.3 59.1 + - + +
22M ASP* 2.6 23.0 + - + -
23M VAL 3.8 0.4 - - - -
24M HIS* 3.0 37.8 + - + +
58M THR* 4.5 7.2 - - + +
72M ARG* 3.7 16.0 - - - +
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Residues in contact with ALA 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L LEU 3.1 15.0 - - - +
69L GLU* 4.1 2.0 - - - -
70L PRO* 3.5 22.9 - - + -
13M VAL* 3.8 1.2 - - - +
14M THR* 1.3 82.3 - - + +
16M VAL* 1.3 69.5 + - - +
17M ILE* 5.5 4.3 - - + -
20M ILE 4.1 0.2 - - - +
21M VAL* 3.5 0.5 - - - -
22M ASP* 2.9 47.8 + - + +
72M ARG* 4.8 2.0 - - - -
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Residues in contact with VAL 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L ALA* 4.2 24.2 - - + -
66L LEU 4.1 1.7 - - - +
67L ASN 3.8 0.3 - - - -
68L LEU* 2.8 52.9 + - + +
13M VAL* 3.8 18.8 - - + -
15M ALA* 1.3 80.5 - - - +
17M ILE* 1.3 64.8 + - - +
18M GLY 4.7 0.7 - - - +
20M ILE 3.7 6.5 - - - +
21M VAL* 3.9 13.5 - - + -
67M THR* 4.2 20.9 - - - +
70M LEU* 3.9 22.4 - - + +
72M ARG* 5.5 2.4 - - + +
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Residues in contact with ILE 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L LEU 4.2 4.7 - - - -
67L ASN* 3.3 32.8 - - + +
68L LEU 4.6 1.6 - - - +
69L GLU* 6.0 6.3 - - + -
289L ARG* 3.3 34.3 - - + +
15M ALA* 5.5 4.5 - - + -
16M VAL* 1.3 80.9 - - - +
18M GLY* 1.3 65.4 + - - +
20M ILE* 3.1 33.5 + - + +
22M ASP* 5.9 2.2 - - - +
271M LEU* 3.9 25.5 - - + +
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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