Contacts of the strand formed by residues 91 - 96 (chain G) in PDB entry 1PV2
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 GLU 91 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G HIS 4.2 5.2 + - - +
50G LYS* 3.3 28.8 - - + -
51G ILE* 2.8 24.4 + - - +
86G HIS* 3.0 37.7 + - + +
89G GLY 3.6 9.5 + - - +
90G PHE* 1.3 77.4 - - - +
92G PHE* 1.3 66.4 + - + +
123G HIS* 5.9 3.1 - - + +
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Residues in contact with PHE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 4.9 3.2 - - - +
51G ILE* 3.3 16.4 - - + +
53G VAL* 4.1 2.9 - - + -
82G LEU* 3.7 43.1 - - + -
86G HIS* 5.7 3.8 - + - -
90G PHE 5.2 1.1 - - - +
91G GLU* 1.3 85.0 - - + +
93G GLU* 1.3 68.8 + - - +
94G VAL* 3.6 29.6 - - + -
119G PHE* 4.2 13.5 - + - -
123G HIS* 3.4 29.2 - + + -
126G LEU* 3.7 35.3 - - + +
127G PHE* 3.6 28.9 - + - -
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Residues in contact with GLU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 3.1 37.8 + - + +
51G ILE 2.9 6.4 + - - +
52G LEU* 3.6 4.5 - - + +
53G VAL* 2.8 26.0 + - - +
92G PHE* 1.3 79.4 - - - +
94G VAL* 1.3 65.7 + - - +
126G LEU* 5.2 11.2 - - + -
131G LYS* 2.8 29.2 + - + +
146G TYR* 2.6 42.3 + - + +
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Residues in contact with VAL 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 4.7 0.9 - - - -
53G VAL* 3.4 13.9 - - + +
55G ALA* 4.1 13.2 - - + -
92G PHE* 3.6 20.6 - - + -
93G GLU* 1.3 75.1 - - - +
95G ALA* 1.3 66.0 + - - +
102G THR* 3.7 18.8 - - - +
126G LEU* 3.5 22.8 + - - +
127G PHE* 3.5 30.1 - - + -
130G PRO* 3.5 18.0 - - + +
131G LYS* 3.1 26.3 + - - +
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Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 4.0 14.6 - - + -
53G VAL 2.9 8.8 + - - +
54G ILE* 3.3 8.2 - - - +
55G ALA 3.2 20.6 + - - -
94G VAL* 1.3 77.0 - - - +
96G THR* 1.3 64.6 + - - +
130G PRO* 4.0 0.2 - - - -
131G LYS* 3.1 15.5 - - + +
133G LEU* 3.9 25.8 - - + -
136G VAL* 4.0 14.6 - - + -
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Residues in contact with THR 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ILE* 5.4 0.4 - - - -
55G ALA* 3.7 25.8 - - + +
56G ALA 4.3 2.7 - - - +
57G ASP* 3.9 17.7 - - + +
95G ALA* 1.3 76.2 - - - +
97G ILE* 1.3 60.0 + - - +
99G GLY* 3.1 17.4 + - - -
100G LEU 2.9 28.5 + - - +
102G THR* 4.3 10.3 - - - +
130G PRO* 3.8 14.6 - - + +
131G LYS 2.9 6.7 + - - +
132G LYS* 3.4 1.4 - - - -
133G LEU* 2.7 33.2 + - - -
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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