Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 6QPA
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 ASN 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B THR* 3.8 12.4 + - - +
38B SER* 3.4 18.7 + - - -
39B HIS* 5.9 0.2 - - - +
91B MET* 3.0 32.2 + - - +
92B HIS 3.6 2.9 - - - -
94B ASP* 1.3 86.8 - - - +
96B PHE* 1.3 64.5 + - - +
98B GLU* 3.2 22.6 + - + +
99B ILE* 2.9 36.2 + - + +
219C LYS* 2.6 32.5 + - - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B HIS* 3.0 18.0 + - - +
93B HIS 3.2 13.3 + - - +
94B ASP 3.5 0.6 - - - -
95B ASN* 1.3 77.9 - - - +
97B LYS* 1.3 64.8 + - + +
98B GLU* 3.8 0.2 + - - -
99B ILE* 3.9 4.3 - - + +
100B PHE* 2.8 40.0 + + + +
207B ILE* 4.0 30.7 - - + -
210B PHE* 6.0 3.6 - + - -
212B LEU* 4.6 13.7 - - + -
228B PRO* 4.7 3.8 - - + -
229B PRO* 3.2 46.2 - - + -
230B GLU 4.1 1.3 - - - -
231B TYR* 3.7 40.8 - + + -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN 3.3 0.4 - - - -
96B PHE* 1.3 82.0 - - + +
98B GLU* 1.3 72.7 + - - +
100B PHE* 3.4 3.3 + - - +
101B GLU* 3.0 21.8 + - - +
225B GLY 4.8 1.2 - - - +
228B PRO* 3.6 33.7 - - + +
227C ASN* 3.2 32.8 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B THR* 4.8 6.5 - - + -
94B ASP 4.0 4.9 - - - +
95B ASN* 3.2 47.7 - - + +
96B PHE 3.8 0.3 + - - -
97B LYS* 1.3 91.2 + - - +
99B ILE* 1.3 64.1 + - - +
101B GLU* 3.1 3.7 + - - +
102B LEU* 2.9 30.7 + - - +
219C LYS* 4.9 13.8 - - + +
222C SER* 3.5 23.1 - - - +
223C THR* 5.4 0.2 - - - -
227C ASN* 3.9 26.5 - - + +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 5.3 12.3 - - + -
35B THR* 3.5 20.6 - - + +
36B THR* 5.2 1.8 - - - +
91B MET* 3.7 31.6 - - + -
92B HIS* 3.9 31.9 - - + +
95B ASN* 2.9 23.1 + - + +
96B PHE* 4.0 5.2 - - + +
98B GLU* 1.3 75.6 - - - +
100B PHE* 1.3 59.0 + - - +
102B LEU* 3.8 6.5 - - + +
103B CSS 2.8 45.1 + - + +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 2.8 27.4 + + + +
97B LYS 3.7 3.8 - - - +
99B ILE* 1.3 78.5 - - - +
101B GLU* 1.3 64.6 + - - +
103B CSS 4.3 3.1 - - + +
104B SER* 2.9 46.3 + - - -
107B LEU* 6.1 0.2 - - + -
210B PHE* 3.5 40.2 - + - -
220B ALA* 3.6 23.8 - - + -
223B THR* 3.6 22.9 - - + -
225B GLY* 3.7 14.4 - - - -
228B PRO* 3.6 29.2 - - + -
229B PRO* 3.6 21.8 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS 3.0 13.9 + - - +
98B GLU* 3.1 7.1 + - - +
100B PHE* 1.3 78.1 - - - +
102B LEU* 1.3 64.5 + - - +
104B SER* 3.5 8.7 + - - -
105B GLY 3.6 6.6 + - - -
224B LEU 5.2 0.3 - - - +
225B GLY* 3.5 28.9 - - - +
223C THR* 2.6 27.7 + - - -
224C LEU* 2.9 40.7 + - + +
225C GLY 3.1 1.9 + - - -
226C ALA* 3.0 30.7 + - + +
227C ASN* 2.9 14.5 + - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.4 29.6 - - + +
31B LYS* 3.8 37.5 - - + +
32B VAL* 4.0 11.4 - - + +
35B THR* 3.6 23.3 - - + +
98B GLU 2.9 19.5 + - - +
99B ILE* 3.8 4.5 - - + +
101B GLU* 1.3 76.9 - - - +
103B CSS 1.3 62.6 + - - +
105B GLY* 3.1 13.0 + - - -
106B CYS 3.5 3.1 + - - -
222C SER 3.4 22.9 - - - +
223C THR* 4.2 5.4 - - - -
224C LEU* 3.8 28.8 - - + +
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Residues in contact with CSS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 4.1 22.4 - - - -
78B GLN* 5.7 5.8 - - - -
99B ILE* 2.8 37.1 + - + +
100B PHE* 4.3 3.1 - - - +
102B LEU* 1.3 71.5 + - - +
104B SER* 1.3 60.3 + - - +
106B CYS* 2.8 46.0 + - - +
107B LEU* 2.9 22.5 + - + +
210B PHE* 5.9 7.9 - - + -
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 2.9 44.9 + - - -
101B GLU 3.7 5.8 - - - -
102B LEU 3.2 0.2 - - - -
103B CSS 1.3 76.0 + - - +
105B GLY* 1.3 63.2 + - - +
107B LEU* 3.5 24.1 + - - +
108B GLY 4.3 2.1 + - - -
220B ALA 5.1 1.7 + - - -
223B THR 5.2 1.2 + - - -
224B LEU 3.6 24.1 - - - -
225B GLY* 3.7 4.7 + - - -
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 5.2 9.3 + - - +
27B LYS* 6.2 1.3 - - - -
28B VAL* 5.2 9.2 - - - -
101B GLU 3.6 4.6 + - - -
102B LEU 3.1 9.5 + - - -
103B CSS 3.1 0.8 - - - -
104B SER* 1.3 80.1 - - - +
106B CYS* 1.3 59.0 + - - +
107B LEU 3.5 0.3 + - - -
108B GLY* 3.7 8.8 + - - -
109B MET* 5.0 0.5 + - - +
224B LEU 5.3 0.2 + - - -
224C LEU* 5.2 6.7 - - - -
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Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 5.0 6.5 - - - -
25B MET* 6.1 0.7 - - - -
28B VAL* 3.6 31.4 - - - -
29B GLY* 5.5 1.3 - - - -
32B VAL* 5.5 0.2 - - - -
102B LEU 4.0 0.7 - - - -
103B CSS 2.8 44.9 + - - +
105B GLY* 1.3 69.2 - - - +
107B LEU* 1.3 62.3 + - + +
108B GLY 3.1 3.4 - - - -
109B MET* 3.0 46.4 + - + +
110B VAL* 3.4 11.0 - - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 6.1 0.2 - - + -
103B CSS 2.9 20.8 + - + +
104B SER* 3.9 17.9 - - - +
105B GLY 3.3 1.0 - - - -
106B CYS* 1.3 77.7 - - + +
108B GLY* 1.3 61.4 + - - +
109B MET 3.0 2.0 + - - -
110B VAL* 3.1 41.5 + - + +
113B GLY 5.3 0.9 - - - +
114B PRO* 4.9 13.5 - - + -
210B PHE* 4.4 32.1 - - + -
220B ALA 6.0 1.6 - - - +
221B VAL* 6.2 4.0 - - + -
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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