Contacts of the strand formed by residues 76 - 82 (chain A) in PDB entry 1P4V
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ILE 3.4 5.2 - - - +
70A MET* 3.4 32.1 - - + -
74A TYR 4.3 5.2 - - - +
75A ASN* 1.3 80.9 - - - +
77A GLY* 1.3 59.2 - - - +
96A MET* 3.3 21.7 - - - +
102A VAL* 3.4 44.0 - - + +
187A ILE* 3.9 20.6 - - + -
510C ILE* 3.7 25.6 - - + -
511C ARG* 3.6 31.6 + - + +
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Residues in contact with GLY 77 (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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68A CYS* 3.0 4.9 - - - +
69A ILE* 2.8 34.4 + - - +
76A ILE* 1.3 77.0 - - - +
78A SER* 1.3 63.1 + - - -
92A ALA* 3.2 26.6 - - - +
95A VAL* 4.4 0.4 - - - -
96A MET* 3.6 9.4 - - - +
102A VAL 3.5 5.2 - - - -
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Residues in contact with SER 78 (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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67A ALA 3.2 5.2 - - - -
68A CYS* 3.7 5.4 - - - -
77A GLY* 1.3 76.7 - - - -
79A VAL* 1.3 69.9 + - - +
92A ALA* 3.9 3.7 + - - +
95A VAL* 4.0 5.3 - - - +
102A VAL 2.8 16.8 + - - -
103A MET* 3.3 19.5 - - - +
104A LEU 3.1 22.0 + - - -
185A PRO* 2.8 36.3 + - - +
187A ILE* 5.4 5.4 - - - -
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Residues in contact with VAL 79 (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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65A LEU 5.0 0.4 - - - +
66A ASP* 3.3 1.7 - - - -
67A ALA 2.8 39.1 + - - +
78A SER* 1.3 81.5 + - - +
80A ALA* 1.3 61.9 + - - +
82A MET* 3.9 13.0 - - + -
88A PRO* 3.5 39.0 - - + +
91A VAL* 3.7 26.5 - - + -
92A ALA* 4.0 4.7 - - + +
95A VAL* 3.8 13.7 - - + -
103A MET* 5.3 0.2 - - - -
104A LEU* 3.2 11.2 - - + +
109A ALA* 4.4 11.2 - - + -
185A PRO* 3.4 3.1 - - - +
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Residues in contact with ALA 80 (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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65A LEU 3.7 1.1 - - - -
66A ASP* 3.5 7.9 - - - +
79A VAL* 1.3 75.0 - - - +
81A CYS* 1.3 70.5 + - - +
82A MET* 3.2 3.2 + - - +
103A MET* 3.9 16.4 - - + -
104A LEU 3.1 7.5 + - - -
105A VAL* 3.1 22.0 - - + +
106A GLY 3.0 19.9 + - - -
181A VAL* 3.9 19.5 - - + -
185A PRO* 3.9 8.5 - - + -
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Residues in contact with CYS 81 (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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64A THR* 3.7 33.4 - - - +
65A LEU 2.9 2.4 + - - -
66A ASP* 2.8 17.7 + - - +
80A ALA* 1.3 72.9 - - - +
82A MET* 1.3 59.6 + - - +
83A GLU* 4.1 3.3 + - - +
106A GLY* 3.2 22.1 - - - +
178A HIS* 4.7 7.6 - - - -
179A GLY* 3.6 30.1 - - - -
180A ARG 5.1 1.1 - - - +
181A VAL* 4.5 5.4 - - + -
405C VAL* 3.7 23.6 - - + -
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Residues in contact with MET 82 (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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63A VAL 3.9 0.9 - - - +
64A THR* 3.4 1.0 - - - -
65A LEU* 2.9 37.9 + - - +
79A VAL* 3.9 8.5 - - + -
80A ALA 4.2 2.5 - - - +
81A CYS* 1.3 76.9 - - - +
83A GLU* 1.3 73.3 + - - +
85A ILE* 3.7 23.9 + - + +
88A PRO* 3.5 38.1 - - + -
91A VAL* 3.6 26.7 - - + -
106A GLY 4.5 4.3 - - - -
109A ALA* 3.7 36.6 - - + +
110A LEU* 4.0 13.5 - - - +
113A ALA* 4.2 0.2 - - - -
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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