Contacts of the helix formed by residues 85 - 95 (chain G) in PDB entry 3PHW
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 SER 85 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G GLY 3.4 2.1 + - - -
84G LEU* 1.3 75.0 - - - +
86G LEU* 1.3 65.9 + - - +
87G GLU* 3.9 6.8 + - - +
88G ASP* 3.4 28.0 + - - +
89G TYR* 2.9 19.6 + - - +
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Residues in contact with LEU 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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69G ALA* 4.0 19.5 - - + +
70G ARG* 4.1 34.5 - - + +
73G TYR* 3.9 33.0 - - + -
74G GLN* 4.2 24.3 - - + +
84G LEU 3.7 1.0 + - - -
85G SER* 1.3 70.3 - - - +
87G GLU* 1.3 67.8 + - + +
89G TYR* 2.8 14.9 + - + -
90G LEU* 2.8 42.9 + - + +
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Residues in contact with GLU 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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70G ARG* 5.7 7.6 - - - +
85G SER* 3.4 6.6 + - - +
86G LEU* 1.3 82.9 - - + +
88G ASP* 1.3 63.3 + - - +
90G LEU* 4.1 7.3 - - - +
91G LYS* 3.3 22.7 + - - +
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Residues in contact with ASP 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 LEU* 4.2 23.0 - - + +
85G SER* 3.2 21.2 + - - +
86G LEU 3.1 1.0 - - - -
87G GLU* 1.3 77.5 - - - +
89G TYR* 1.3 66.8 + - - +
91G LYS* 3.3 8.6 + - - +
92G ARG* 2.9 24.4 + - - +
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Residues in contact with TYR 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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65G THR* 4.3 1.7 - - - +
69G ALA* 3.8 19.1 - - + -
73G TYR* 3.4 47.8 - + + +
82G VAL* 4.5 13.2 - - + -
84G LEU* 3.9 14.0 - - + +
85G SER 2.9 12.4 + - - +
86G LEU* 2.8 13.3 + - + +
88G ASP* 1.3 71.3 - - - +
90G LEU* 1.3 70.7 + - + +
92G ARG* 2.9 4.7 + - + +
93G MET* 2.8 49.3 + - + +
103G LEU* 4.0 11.3 - - + +
104G GLU* 2.9 34.0 + - - +
107G MET* 3.2 20.5 - - + +
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Residues in contact with LEU 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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66G GLU* 3.8 24.5 - - + +
69G ALA* 3.4 30.1 - - + -
70G ARG* 3.4 44.2 - - + +
86G LEU* 2.8 41.7 + - + +
87G GLU* 4.1 6.3 - - - +
89G TYR* 1.3 75.5 - - + +
91G LYS* 1.3 62.6 + - - +
93G MET* 3.3 11.1 + - + +
94G LEU* 3.0 36.6 + - + +
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Residues in contact with LYS 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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87G GLU 3.3 17.2 + - - +
88G ASP* 3.3 11.4 + - - +
89G TYR 3.1 0.4 - - - -
90G LEU* 1.3 80.0 - - - +
92G ARG* 1.3 60.0 + - - +
94G LEU* 3.8 6.7 + - + +
95G SER* 2.8 21.8 + - - -
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Residues in contact with ARG 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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92A ARG* 6.2 3.8 - - + +
95A SER* 3.1 25.3 + - - -
96A ASP* 3.0 32.7 + - - +
97A ASN* 4.2 4.9 + - - +
98A GLU* 3.0 30.3 + - - +
84G LEU* 3.8 30.9 - - + +
88G ASP 2.9 12.2 + - - +
89G TYR* 3.5 7.9 - - + +
91G LYS* 1.3 74.4 - - - +
93G MET* 1.3 65.9 + - - +
95G SER* 3.1 16.8 + - - +
98G GLU* 3.0 46.2 - - - +
74H ARG* 6.0 0.2 - - - +
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Residues in contact with MET 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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42G TYR* 3.6 18.3 + - - +
62G LYS* 2.7 46.8 + - - +
65G THR* 3.9 17.5 - - + -
66G GLU* 3.6 35.2 - - - +
89G TYR* 2.8 44.4 + - + +
90G LEU* 3.6 17.9 - - + +
92G ARG* 1.3 74.6 - - - +
94G LEU* 1.3 73.3 + - + +
95G SER 3.2 1.7 + - - +
98G GLU* 3.9 12.0 - - - +
104G GLU* 4.5 2.7 - - - +
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Residues in contact with LEU 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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62G LYS* 3.3 29.4 + - + +
63G ARG* 5.5 1.1 - - - -
66G GLU* 4.0 27.4 - - + +
90G LEU* 3.0 24.6 + - + +
91G LYS* 4.3 6.5 - - + +
92G ARG 3.4 0.2 - - - -
93G MET* 1.3 96.3 - - + +
95G SER* 1.3 64.1 + - - +
96G ASP* 3.6 1.6 + - - -
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Residues in contact with SER 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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92A ARG* 3.9 21.1 - - - -
62G LYS* 2.9 17.7 + - - -
91G LYS 2.8 19.5 + - - -
92G ARG* 3.1 15.6 + - - +
93G MET 3.2 1.6 - - - -
94G LEU* 1.3 76.7 - - - +
96G ASP* 1.3 65.3 + - - +
98G GLU* 3.4 14.1 + - - +
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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