Contacts of the strand formed by residues 6 - 12 (chain A) in PDB entry 4PEI
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 ILE 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLN* 1.3 81.7 - - - +
7A GLN* 1.3 69.4 + - - +
8A HIS* 3.6 36.6 + - + +
260A ASP* 4.0 10.3 - - + -
261A LEU 3.3 19.5 - - - +
262A PRO* 5.2 1.6 - - + -
263A LEU* 4.1 8.7 - - - +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 1.3 75.4 - - - +
8A HIS* 1.3 58.8 + - - +
9A ILE* 3.8 21.4 + - + +
38A SER* 3.2 18.1 + - - +
39A PHE* 3.8 4.5 - - - -
122A ASN* 2.8 51.5 + - - +
124A LEU* 3.8 13.6 - - - +
259A LEU 3.3 3.3 - - - +
260A ASP* 3.6 0.9 - - - -
261A LEU* 2.7 49.0 + - + +
262A PRO 3.3 19.0 + - - +
263A LEU* 3.8 17.0 - - + +
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Residues in contact with HIS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.6 31.0 + - + +
7A GLN* 1.3 73.2 - - - +
9A ILE* 1.3 62.4 + - - +
29A TYR* 3.7 20.9 + - + +
35A LYS* 3.4 37.0 - - + +
36A GLU 3.3 25.9 + - - +
37A ILE* 3.6 5.5 - - - -
38A SER* 2.8 33.5 + - - -
258A TYR* 5.4 1.8 - - + -
259A LEU 3.5 3.6 - - - -
260A ASP* 2.6 27.6 + - + +
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLN* 3.8 15.5 - - + +
8A HIS* 1.3 77.6 - - - +
10A ALA* 1.3 69.3 + - - +
11A ILE* 3.4 5.1 + - + +
38A SER* 4.8 0.4 - - - -
39A PHE* 3.5 45.3 - - + +
41A ILE* 3.7 28.3 - - + -
124A LEU* 3.6 22.4 - - + -
176A ILE* 4.8 4.3 - - + -
258A TYR* 3.3 5.5 - - - +
259A LEU* 2.9 42.7 + - + +
261A LEU* 3.9 17.3 - - + -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS 4.1 1.6 + - - -
9A ILE* 1.3 72.8 - - - +
11A ILE* 1.3 62.0 + - - +
12A VAL* 4.9 0.4 - - + -
26A LEU* 3.6 30.3 - - + -
37A ILE* 4.4 7.6 - - + +
39A PHE 3.0 7.2 + - - +
40A VAL* 3.4 20.8 - - + -
41A ILE 2.8 28.1 + - - +
256A ILE* 4.7 1.8 - - + -
257A SER 3.5 6.3 - - - +
258A TYR* 3.7 15.1 - - + -
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.4 2.6 + - + +
10A ALA* 1.3 75.9 - - - +
12A VAL* 1.3 61.4 + - - +
41A ILE* 3.5 17.3 - - + +
227A ILE* 3.4 31.2 - - + -
245A ILE* 4.2 19.1 - - + -
247A LEU* 3.3 19.2 - - + +
256A ILE* 3.3 3.7 - - - -
257A SER* 2.8 70.0 + - - +
258A TYR* 3.8 2.5 - - - +
259A LEU* 3.9 35.2 - - + -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.6 1.6 - - + -
11A ILE* 1.3 81.0 - - - +
13A GLY* 1.3 71.5 + - - +
15A VAL* 4.2 3.1 - - + -
22A MET* 3.9 15.5 - - + -
26A LEU* 5.0 0.9 - - + -
40A VAL* 3.7 22.9 - - + -
41A ILE 2.8 16.9 + - - +
42A CYS* 3.5 8.6 - - - -
43A THR* 2.9 29.5 + - - +
247A LEU* 3.6 5.1 - - - +
250A ILE* 3.7 33.2 - - + -
255A ALA 3.2 5.8 - - - +
256A ILE* 4.4 14.4 - - + -
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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