Contacts of the helix formed by residues 87 - 98 (chain G) in PDB entry 3X0X
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 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31G TRP* 5.2 0.2 - - + -
35G ALA* 5.1 3.3 - - - +
38G ARG* 2.4 42.2 + - - +
39G ASP 5.8 0.5 + - - -
83G ILE 2.9 9.5 + - - +
84G ALA* 3.2 5.0 + - - +
86G ALA* 1.3 82.6 - - + +
88G GLY* 1.3 65.0 + - - +
89G SER* 2.8 28.7 + - - -
90G LEU* 3.1 24.5 + - + -
91G GLY 2.9 18.7 + - - -
212G GLN* 4.4 0.9 - - - +
380G ARG* 6.3 0.2 - - - +
384G ASN* 5.1 1.1 + - - -
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Residues in contact with GLY 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 ALA* 3.6 4.0 + - - -
87G ASP* 1.3 73.0 + - - +
89G SER* 1.3 57.2 + - - +
91G GLY* 3.2 2.9 + - - -
92G HIS* 3.1 23.2 + - - +
210G MET* 3.7 14.8 - - - +
261G VAL* 4.1 2.6 - - - +
265G ILE* 3.8 25.7 - - - +
384G ASN* 3.6 23.7 - - - +
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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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87G ASP* 2.8 11.1 + - - -
88G GLY* 1.3 73.5 - - - +
90G LEU* 1.3 62.0 + - - +
92G HIS 3.4 0.3 + - - -
93G LEU* 3.0 30.0 + - - +
210G MET* 3.2 19.1 - - - -
211G ARG 3.4 1.2 + - - -
212G GLN* 2.9 47.6 + - - +
213G THR* 3.5 15.4 - - - +
384G ASN* 4.4 4.5 + - - +
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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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31G TRP* 3.5 43.1 - - + -
38G ARG* 4.1 2.2 - - - +
45G ALA* 3.8 29.2 - - + +
48G GLU* 3.9 22.9 - - + -
49G ARG* 5.1 0.7 - - + +
52G LEU* 5.0 7.1 - - + +
83G ILE* 3.6 13.0 - - + +
87G ASP* 3.1 30.9 + - + +
89G SER* 1.3 81.0 - - - +
91G GLY* 1.3 60.4 + - - +
93G LEU* 3.8 14.8 - - + +
94G PHE* 2.9 32.9 + - - +
212G GLN* 5.2 2.0 - - - +
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Residues in contact with GLY 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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80G VAL* 4.0 4.1 - - - +
83G ILE* 3.5 15.7 - - - +
84G ALA* 3.9 20.4 - - - -
87G ASP 2.9 10.9 + - - -
88G GLY 3.6 4.0 - - - -
90G LEU* 1.3 77.3 - - - +
92G HIS* 1.3 51.8 + - - +
94G PHE* 4.2 0.6 - - - +
95G GLY* 2.8 33.1 + - - -
261G VAL* 3.8 11.9 - - - +
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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
----------------------------------------------------------
88G GLY 3.1 12.7 + - - +
89G SER 3.8 6.3 - - - +
91G GLY* 1.3 71.7 - - - +
93G LEU* 1.3 68.4 + - - +
96G TYR* 3.0 60.9 + + + +
163G SER* 4.2 10.1 - - - -
210G MET* 4.3 12.1 - - + +
213G THR* 3.5 26.4 + - + +
215G SER* 4.2 13.5 - - - -
258G PHE* 4.1 9.9 - + - -
261G VAL* 4.1 12.6 - - + +
388G HIS* 3.1 46.1 + + - -
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Residues in contact with LEU 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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49G ARG* 3.3 52.9 - - + +
52G LEU* 5.7 0.2 - - + -
89G SER 3.0 19.1 + - - +
90G LEU* 3.8 12.8 - - + +
92G HIS* 1.3 79.8 - - - +
94G PHE* 1.3 63.7 + - - +
96G TYR* 4.0 2.3 - - - +
97G HIS* 3.0 23.9 + - - +
126G TRP* 3.8 20.4 - - + -
163G SER 5.6 0.2 - - - -
164G GLY* 4.3 11.9 - - - +
212G GLN 4.4 8.7 - - - +
213G THR* 3.2 33.4 - - - +
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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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52G LEU* 4.2 19.5 - - + -
57G LEU* 3.3 45.8 - - + -
58G LEU* 4.2 9.0 - - + -
60G LEU* 4.1 5.2 - - + -
79G VAL* 3.6 24.5 - - + -
80G VAL* 4.6 7.9 - - - -
83G ILE* 3.2 23.8 - - + -
90G LEU 2.9 18.3 + - - +
91G GLY 4.2 0.7 - - - +
93G LEU* 1.3 79.1 - - - +
95G GLY* 1.3 64.7 + - - +
97G HIS* 2.9 15.2 + + - +
98G LEU* 2.9 53.7 + - + +
126G TRP* 4.3 6.2 - + - -
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Residues in contact with GLY 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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80G VAL* 3.8 18.8 - - - -
91G GLY 2.8 22.1 + - - -
92G HIS 4.1 0.4 - - - -
94G PHE* 1.3 74.1 - - - +
96G TYR* 1.3 57.4 + - - +
98G LEU* 3.4 12.4 + - - +
99G THR* 3.2 20.6 - - - +
257G ILE* 3.5 25.3 - - - +
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Residues in contact with TYR 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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92G HIS* 3.0 45.7 + + + +
93G LEU* 4.0 3.4 - - - +
95G GLY* 1.3 74.2 - - - +
97G HIS* 1.3 67.7 + - - +
98G LEU 3.2 0.2 - - - -
99G THR* 3.1 31.2 + - + -
100G ASN* 3.5 9.0 - - - +
129G ASN* 3.4 29.1 + - - -
131G SER* 5.1 2.6 + - - -
134G ASN* 5.7 1.0 + - - -
163G SER* 2.9 31.5 + - - -
250G PHE* 5.1 11.6 - + - -
254G ALA* 5.2 6.4 - - + +
257G ILE* 4.4 2.2 - - - +
258G PHE* 4.0 27.9 - + + -
388G HIS* 5.2 1.1 - - - -
391G HIS* 4.6 11.3 + + - -
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Residues in contact with HIS 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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58G LEU* 2.6 51.6 + - + -
93G LEU 3.0 14.2 + - - +
94G PHE* 2.9 13.6 + + - +
96G TYR* 1.3 76.5 - - - +
98G LEU* 1.3 76.4 + - + +
99G THR 3.0 1.9 + - - -
100G ASN* 3.3 14.3 + - - -
101G ALA* 4.5 2.1 + - - +
120G ILE* 5.5 5.6 - - + -
125G TRP 3.5 21.3 - - - -
126G TRP* 3.8 11.1 - + + -
127G THR* 2.7 58.8 + - + +
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Residues in contact with LEU 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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58G LEU 4.4 4.3 - - - +
60G LEU* 3.8 27.8 - - + -
61G LEU* 3.3 32.4 - - + +
76G ALA* 4.1 13.2 - - + +
80G VAL* 4.1 19.1 - - + -
94G PHE* 2.9 47.9 + - + +
95G GLY 3.4 9.2 - - - +
96G TYR 3.2 0.4 - - - -
97G HIS* 1.3 94.1 - - + +
99G THR* 1.3 57.2 + - - +
100G ASN 3.4 0.4 - - - -
101G ALA* 5.4 0.4 - - - +
102G PRO* 3.3 17.5 - - - +
257G ILE* 4.8 4.5 - - + -
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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