Contacts of the helix formed by residues 81 - 93 (chain G) in PDB entry 2P5V
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 ASP 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G ALA 3.2 1.6 + - - -
80G LYS* 1.3 96.7 + - - +
82G ALA* 1.3 63.5 + - - +
83G ARG 3.4 2.0 - - - +
84G GLU* 3.9 31.5 - - + +
85G ASP* 2.9 40.1 + - - +
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Residues in contact with ALA 82 (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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76G ILE* 4.0 6.9 - - + +
77G ARG* 3.0 31.9 - - + +
79G ALA* 3.1 17.9 + - + +
80G LYS 3.1 3.8 + - - -
81G ASP* 1.3 76.9 - - - +
83G ARG* 1.3 64.1 + - + +
85G ASP* 3.9 3.1 - - - +
86G PHE* 3.0 26.7 + - - +
132G HIS* 5.5 2.5 - - + -
133G GLY* 4.1 22.2 - - - -
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Residues in contact with ARG 83 (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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125E LEU* 3.8 21.2 - - - +
129E LEU* 3.3 36.3 - - - +
136E ASP* 5.3 2.8 + - - -
76G ILE* 4.0 27.3 - - + +
79G ALA 4.9 0.2 + - - -
81G ASP* 3.4 1.0 - - - +
82G ALA* 1.3 76.9 - - + +
84G GLU* 1.3 58.7 + - - +
86G PHE* 3.3 1.9 + - - +
87G ALA* 3.0 31.6 + - - +
101G ALA* 4.2 9.3 - - - +
107G ASP* 4.1 26.5 + - - +
108G TYR* 3.0 45.2 + - - +
143H LEU* 5.8 1.6 - - - +
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Residues in contact with GLU 84 (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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81G ASP* 3.9 35.0 - - + +
82G ALA 3.4 0.4 - - - -
83G ARG* 1.3 79.4 - - - +
85G ASP* 1.3 65.1 + - - +
87G ALA* 3.4 6.1 + - - +
88G ALA* 3.1 23.0 + - + +
91G ARG* 4.7 3.5 + - - +
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Residues in contact with ASP 85 (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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80G LYS 5.0 0.5 - - - +
81G ASP* 2.9 34.4 + - - +
82G ALA 4.0 2.9 - - - +
84G GLU* 1.3 80.1 - - - +
86G PHE* 1.3 59.9 + - - +
88G ALA* 3.5 7.4 + - - +
89G SER* 3.1 27.7 + - - -
131G HIS* 3.4 5.0 + - + -
132G HIS* 3.0 36.8 + - + +
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Residues in contact with PHE 86 (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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74G VAL* 3.9 14.4 - - + -
76G ILE* 3.7 20.4 - - + -
82G ALA 3.0 18.7 + - - +
83G ARG 3.7 1.6 - - - +
85G ASP* 1.3 75.1 - - - +
87G ALA* 1.3 67.5 + - - +
89G SER* 3.2 1.7 + - - -
90G VAL* 2.9 26.4 + - + +
93G TRP* 3.9 17.0 - + - -
99G CYS* 4.2 11.9 - - - -
108G TYR* 3.9 36.3 - + + -
110G LEU* 4.0 21.5 - - + -
128G LEU* 3.9 12.8 - - + -
131G HIS* 3.8 13.2 - - + +
133G GLY* 5.2 0.7 - - - -
134G VAL* 3.6 31.4 - - + -
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Residues in contact with ALA 87 (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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83G ARG 3.0 18.1 + - - +
84G GLU* 3.7 5.4 - - - +
86G PHE* 1.3 78.3 - - + +
88G ALA* 1.3 61.9 - - - +
90G VAL* 3.1 17.8 - - - +
91G ARG* 3.1 31.9 + - - +
108G TYR* 5.7 1.1 - - - +
146H ILE* 3.2 37.7 - - + -
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Residues in contact with ALA 88 (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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84G GLU* 3.1 18.1 + - + +
85G ASP* 3.6 8.7 - - - +
86G PHE 3.2 0.2 - - - -
87G ALA* 1.3 78.1 - - - +
89G SER* 1.3 60.1 + - - +
91G ARG* 3.6 18.7 + - - +
92G LYS* 3.5 30.7 + - - +
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Residues in contact with SER 89 (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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85G ASP 3.1 6.6 + - - -
86G PHE 3.8 2.5 - - - -
88G ALA* 1.3 75.6 - - - +
90G VAL* 1.3 61.5 + - - +
92G LYS* 3.0 24.6 + - - +
93G TRP* 3.2 33.6 + - - +
131G HIS* 2.7 40.6 + - - -
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Residues in contact with VAL 90 (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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86G PHE* 2.9 19.5 + - + +
87G ALA* 3.1 19.5 - - - +
89G SER* 1.3 76.8 - - - +
91G ARG* 1.3 51.7 + - + +
93G TRP* 3.2 28.5 + - + +
96G VAL* 3.6 27.6 - - + -
99G CYS* 4.0 17.9 - - + -
110G LEU* 4.0 13.9 - - + -
146H ILE* 3.5 23.3 - - + -
147H LYS* 2.7 35.6 + - + +
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Residues in contact with ARG 91 (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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84G GLU* 4.7 4.0 + - - +
87G ALA* 3.1 42.4 + - - +
88G ALA* 3.7 15.0 - - - +
89G SER 3.2 0.4 - - - -
90G VAL* 1.3 77.9 - - - +
92G LYS* 1.3 59.7 + - + +
144H LYS* 5.8 4.0 - - - +
145H GLU 5.2 0.6 + - - -
146H ILE* 3.2 43.9 + - + +
147H LYS* 3.6 25.7 + - + +
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Residues in contact with LYS 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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88G ALA* 3.5 21.9 - - - +
89G SER* 3.0 13.7 + - - +
91G ARG* 1.3 79.2 - - + +
93G TRP* 1.3 63.7 + - + +
94G PRO* 3.2 16.4 - - - +
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Residues in contact with TRP 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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86G PHE* 3.9 19.3 - + - -
89G SER* 3.2 31.1 + - - +
90G VAL* 3.2 29.8 + - + +
92G LYS* 1.3 81.0 - - + +
94G PRO* 1.3 64.7 - - + +
95G GLU* 3.2 12.3 - - - +
96G VAL* 3.1 16.2 + - + -
110G LEU* 4.8 1.3 - - + -
123G PHE* 3.8 18.6 - + + -
127G THR* 3.3 33.3 - - + +
128G LEU* 3.8 32.8 - - + -
131G HIS* 4.0 16.8 - + - -
147H LYS* 2.6 24.3 + - - -
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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