Contacts of the helix formed by residues 87 - 94 (chain B) in PDB entry 6FEQ
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B THR 5.4 6.1 - - - -
84B GLY 4.6 2.3 + - - -
85B GLY* 3.1 0.6 - - - -
86B LYS* 1.3 84.0 - - - +
88B SER* 1.3 63.7 + - - +
89B LEU 3.8 0.2 - - - -
90B LEU* 4.3 5.9 - - - +
91B ASP* 2.9 28.8 + - - +
210B ASP* 5.1 12.8 + - - -
241B SER* 5.4 0.7 - - - -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 5.8 0.4 - - - -
63B ILE* 4.8 15.1 - - - +
64B LEU* 4.3 18.2 - - - -
84B GLY 5.1 0.4 + - - -
85B GLY* 3.3 10.9 + - - -
87B SER* 1.3 81.8 - - - +
89B LEU* 1.3 64.7 + - - +
90B LEU 3.2 1.6 - - - -
91B ASP 3.4 0.6 + - - -
92B VAL* 3.2 29.1 + - - +
97B LYS* 3.6 27.1 + - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.8 13.2 - - + -
42B ILE* 5.1 8.5 - - + -
64B LEU* 4.1 15.3 - - + +
67B ILE* 4.1 35.0 - - + -
71B MET* 5.1 3.1 - - + -
78B ILE* 4.0 21.3 - - + -
85B GLY* 2.9 17.9 + - - +
88B SER* 1.3 77.6 - - - +
90B LEU* 1.3 58.1 + - - +
92B VAL* 3.4 5.2 + - + +
93B LEU* 3.0 52.8 + - + +
257B THR* 4.9 4.9 - - + -
259B LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 90 (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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78B ILE* 4.9 10.0 - - + +
85B GLY 4.5 0.8 + - - -
86B LYS 4.1 13.9 + - - +
87B SER* 4.3 6.0 - - - +
88B SER 3.2 1.0 - - - +
89B LEU* 1.3 81.1 - - - +
91B ASP* 1.3 58.7 + - - +
93B LEU* 3.4 3.0 + - + +
94B ALA* 3.0 31.6 + - - +
123B TYR* 4.4 13.2 - - + +
208B PHE* 3.9 13.9 - - + -
209B LEU 3.3 22.2 - - - +
210B ASP* 4.0 26.7 - - + +
239B ILE* 3.7 37.9 - - + +
240B PHE* 4.5 3.6 - - - -
241B SER* 4.5 9.4 - - - +
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Residues in contact with ASP 91 (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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87B SER* 2.9 22.6 + - - +
88B SER 3.4 2.0 + - - +
89B LEU 3.4 0.2 - - - -
90B LEU* 1.3 77.7 - - - +
92B VAL* 1.3 61.5 + - - +
94B ALA* 3.7 1.5 + - - -
95B ALA 3.4 1.6 + - - -
96B ARG* 2.6 45.1 + - + +
97B LYS* 3.5 37.0 + - + -
123B TYR* 3.3 27.4 + - - -
210B ASP* 5.2 1.0 - - - +
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Residues in contact with VAL 92 (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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42B ILE* 4.8 8.7 - - + -
44B TYR* 4.4 22.2 - - + -
64B LEU* 5.1 4.7 - - + -
88B SER 3.2 18.0 + - - +
89B LEU* 3.8 8.1 - - + +
90B LEU 3.3 0.2 - - - -
91B ASP* 1.3 76.8 - - - +
93B LEU* 1.3 68.8 + - + +
95B ALA* 3.0 20.0 + - - +
96B ARG 4.9 0.2 - - - +
97B LYS* 3.8 23.6 - - + +
102B LEU* 3.7 33.8 - - + +
106B VAL* 5.3 3.9 - - + +
113B ARG* 4.6 9.9 + - - -
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Residues in contact with LEU 93 (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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37B LEU* 4.8 19.4 - - + +
39B PHE* 3.7 38.1 - - + -
42B ILE* 5.5 2.5 - - + -
71B MET* 4.0 26.2 - - + -
78B ILE* 6.2 0.4 - - + -
89B LEU* 3.0 46.5 + - + +
90B LEU* 4.1 4.5 - - + +
92B VAL* 1.3 83.7 - - + +
94B ALA* 1.3 56.4 + - - +
95B ALA 3.3 1.1 - - - -
106B VAL* 5.1 13.2 - - + +
113B ARG* 4.8 3.4 - - - +
117B PHE* 3.7 12.5 - - - -
208B PHE* 3.3 22.1 - - + -
239B ILE* 5.3 4.5 - - + -
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Residues in contact with ALA 94 (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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90B LEU 3.0 17.4 + - - +
91B ASP 4.4 0.2 - - - +
92B VAL 3.1 0.2 - - - -
93B LEU* 1.3 76.7 - - - +
95B ALA* 1.3 68.4 + - - +
96B ARG* 3.2 26.3 + - + +
117B PHE* 4.1 6.6 - - - -
118B LYS* 5.1 3.5 - - - +
121B SER* 5.3 2.3 + - - -
123B TYR* 4.2 13.0 - - + -
208B PHE* 3.7 34.3 - - + -
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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