Contacts of the helix formed by residues 91 - 98 (chain G) in PDB entry 3EXF
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 ALA 91 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G THR* 3.8 15.9 - - + -
88G ALA 3.8 19.7 - - - +
89G TYR* 2.9 9.4 + - - +
90G ARG* 1.3 71.9 - - - +
92G HIS* 1.3 69.4 + - - +
93G GLY 3.2 3.6 + - - -
94G PHE* 3.3 7.1 + - - +
95G THR* 2.9 23.8 + - - +
123G SER 5.1 0.7 - - - +
126G MET* 4.3 12.6 - - + -
131G PHE* 4.1 6.7 - - + -
134G GLY* 3.9 12.6 - - - +
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Residues in contact with HIS 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G MET* 4.0 14.6 - - + +
46G GLU* 3.0 37.8 + - - +
62G CYS* 4.3 2.7 - - - -
63G HIS 3.4 20.0 + - - -
64G LEU* 4.0 11.2 - - + -
89G TYR 5.1 1.2 + - - -
90G ARG 3.7 0.8 - - - -
91G ALA* 1.3 79.7 - - - +
93G GLY* 1.3 69.8 + - - +
95G THR* 3.1 15.2 + - - -
96G PHE* 3.3 11.1 + - - +
105G ILE* 4.7 8.7 - - + -
109G LEU* 3.7 23.5 - - + +
123G SER* 2.8 32.9 + - - -
126G MET* 3.8 22.9 - - + -
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Residues in contact with GLY 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 3.8 12.0 - - - +
65G CYS* 3.4 21.1 - - - -
72G CYS* 3.6 26.2 - - - -
90G ARG 4.7 0.6 + - - -
91G ALA 3.2 1.4 + - - -
92G HIS* 1.3 79.2 - - - +
94G PHE* 1.3 57.8 + - - +
96G PHE* 3.3 5.5 + - - +
97G THR* 3.0 26.5 + - - +
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Residues in contact with PHE 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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65G CYS* 6.5 0.7 - - + -
71G CYS* 4.8 0.4 - - + -
72G CYS* 3.7 33.4 - - + +
75G LEU* 3.9 18.6 - - + -
85G LEU* 3.3 31.2 - - + -
87G THR* 4.1 19.1 - - + -
90G ARG 4.3 13.9 - - - -
91G ALA 3.3 8.0 + - - +
93G GLY* 1.3 69.7 - - - +
95G THR* 1.3 69.6 + - - +
96G PHE 3.1 1.8 - - - -
97G THR* 3.2 13.2 - - - -
98G ARG* 2.8 29.1 + - + +
131G PHE* 3.7 18.8 - - + -
164G LEU* 3.4 28.7 - - + -
194G GLU* 4.2 13.7 - - - -
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Residues in contact with THR 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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91G ALA 2.9 17.8 + - - +
92G HIS* 3.1 9.2 + - - -
94G PHE* 1.3 74.2 - - - +
96G PHE* 1.3 58.4 + - - +
98G ARG* 3.6 3.1 + - - +
99G GLY 3.5 3.1 + - - -
100G LEU* 3.1 46.3 + - - +
105G ILE* 3.2 23.2 - - - +
126G MET* 3.7 27.4 - - + +
128G ALA* 4.8 1.3 - - - +
131G PHE* 3.0 35.0 - - + -
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Residues in contact with PHE 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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37G ARG* 6.2 1.1 - - + -
38G MET* 3.9 30.1 - - + -
41G THR* 3.6 35.0 - - + -
42G VAL* 3.8 16.4 - - + -
45G MET* 4.6 9.4 - - + -
92G HIS 3.3 3.7 + - - +
93G GLY 3.3 7.5 + - - +
94G PHE 3.1 0.2 - - - -
95G THR* 1.3 82.7 + - - +
97G THR* 1.3 66.7 + - + +
99G GLY* 3.1 11.1 + - - -
100G LEU 3.6 25.5 - - - +
101G SER* 5.0 1.6 - - - -
102G VAL* 4.1 25.1 - - + -
105G ILE* 3.7 13.7 - - + -
316G GLU* 4.9 4.5 - - - -
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Residues in contact with THR 97 (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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38G MET* 3.8 26.5 - - + +
42G VAL* 4.7 1.6 - - + -
72G CYS* 3.7 35.5 + - + +
73G VAL* 4.0 10.8 - - + -
76G GLU* 3.2 29.8 + - - +
93G GLY 3.0 16.4 + - - +
94G PHE* 3.2 24.1 + - - +
96G PHE* 1.3 83.6 - - + +
98G ARG* 1.3 56.7 + - - +
99G GLY 3.2 2.7 + - - -
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Residues in contact with ARG 98 (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 GLU* 2.8 38.7 + - - +
79G ILE* 3.6 12.4 - - - +
80G ASN 3.1 23.0 + - - -
81G PRO* 3.4 13.8 + - - +
83G ASP 2.7 26.9 + - - -
84G HIS* 4.3 1.6 - - - +
85G LEU* 3.8 27.6 - - - +
94G PHE* 2.8 21.4 + - - +
95G THR* 3.8 3.1 - - - +
97G THR* 1.3 73.1 - - - +
99G GLY* 1.3 56.9 + - - +
100G LEU 3.7 2.2 + - - -
128G ALA* 4.3 7.4 - - + +
129G LYS* 3.7 16.7 + - - +
130G ASN* 3.4 21.6 + - - +
131G PHE* 3.4 28.3 - - + -
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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