Contacts of the strand formed by residues 12 - 18 (chain K) in PDB entry 5OGC
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 MET 12 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K HIS* 2.9 28.8 + - + +
11K HIS* 1.3 95.7 + - + +
13K LYS* 1.3 73.5 + - - +
14K VAL* 4.1 19.3 - - + -
77K ASP* 4.2 3.8 - - - +
292K ILE* 6.3 2.2 - - + -
295K LEU* 4.5 21.1 - - + -
299K LYS* 5.2 9.0 - - + -
320K LEU* 5.9 0.7 - - + -
326K THR* 3.4 39.0 - - + +
328K MET* 4.3 9.0 - - + -
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Residues in contact with LYS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K HIS 5.0 4.7 - - - +
11K HIS 4.3 3.6 - - - +
12K MET* 1.3 76.2 - - - +
14K VAL* 1.3 73.6 + - - +
77K ASP* 3.2 38.2 + - - +
78K ALA* 5.3 1.3 - - + +
92K HIS* 4.5 17.0 - - + +
96K PRO* 5.5 11.6 - - + +
326K THR 3.2 6.6 + - - +
327K ILE* 3.2 40.9 - - + -
328K MET 3.6 1.7 + - - -
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Residues in contact with VAL 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K MET* 4.1 17.5 - - + -
13K LYS* 1.3 83.6 - - - +
15K VAL* 1.3 58.8 + - - +
76K PHE* 3.3 49.1 - - + -
77K ASP* 3.5 17.3 + - + +
78K ALA 3.1 24.4 + - - +
327K ILE* 4.5 0.2 - - - -
328K MET* 3.7 22.2 - - + +
349K ALA 5.9 1.3 - - - +
353K LYS* 5.5 12.3 - - + -
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Residues in contact with VAL 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K VAL* 1.3 74.2 - - - +
16K VAL* 1.3 67.4 + - - +
17K ARG* 4.9 0.7 - - + +
76K PHE* 4.0 0.4 - - - -
78K ALA* 3.2 26.0 - - + +
79K VAL* 4.2 1.1 - - - -
80K PHE* 4.1 26.9 - - + +
89K VAL* 5.0 1.8 - - + -
92K HIS* 3.7 17.9 - - + +
93K THR* 3.1 28.0 - - - +
327K ILE* 3.4 15.0 - - + +
328K MET 2.9 21.2 + - - +
329K ILE* 3.2 19.9 - - + +
330K ALA 3.6 0.3 + - - -
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Residues in contact with VAL 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 1.3 75.4 - - - +
17K ARG* 1.3 60.3 + - - +
18K VAL 4.4 0.2 - - - +
42K LEU* 5.3 3.4 - - + -
76K PHE* 3.2 31.6 - - + -
78K ALA 3.5 6.9 + - - -
79K VAL* 3.1 22.3 - - + +
80K PHE 3.1 17.4 + - - +
330K ALA* 3.5 28.5 - - + +
332K VAL* 3.7 39.3 - - + -
346K LEU* 4.3 15.9 - - + -
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Residues in contact with ARG 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 3.9 3.3 + - + +
16K VAL* 1.3 71.6 - - - +
18K VAL* 1.3 65.0 + - - +
19K ARG* 3.1 31.4 + - - +
80K PHE* 3.4 9.0 - - + -
84K SER* 2.9 33.0 - - - +
85K THR 2.9 1.0 - - - -
86K GLN* 2.7 66.8 + - - +
89K VAL* 3.2 33.9 - - + +
123K MET* 3.2 28.1 - - - +
132K VAL* 3.7 7.5 - - - +
329K ILE* 4.2 7.7 - - + +
330K ALA 3.0 14.6 + - - +
331K ALA* 4.0 4.0 - - - -
332K VAL* 3.8 11.4 + - - -
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Residues in contact with VAL 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K VAL* 3.5 3.5 + - + +
17K ARG* 1.3 81.7 - - - +
19K ARG* 1.3 65.8 + - - +
34K VAL* 5.9 1.1 - - + -
36K VAL* 3.4 32.3 - - + -
42K LEU* 5.9 1.6 - - + -
79K VAL* 4.7 6.5 - - + -
80K PHE 2.9 17.1 + - - +
81K ASP* 3.0 20.2 - - - +
82K GLU* 3.3 30.5 - - + +
84K SER 3.7 1.2 - - - +
332K VAL* 3.1 34.9 - - + +
333K SER 4.8 0.2 - - - -
334K PRO* 4.0 15.9 - - + -
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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