Contacts of the strand formed by residues 178 - 184 (chain B) in PDB entry 5FQD
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 GLN 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B PRO* 3.6 4.3 - - - +
83B VAL* 3.0 59.9 + - + +
85B PRO* 5.9 5.7 - - + +
123B LEU* 4.2 8.9 - - - +
125B TYR* 4.0 12.3 + - - -
131B ARG* 5.4 9.8 - - - +
170B LEU* 4.2 22.0 - - - +
171B ARG 3.4 12.6 - - - +
172B THR* 3.6 20.6 + - - +
176B GLY 4.0 2.3 + - - +
177B ILE* 1.3 77.9 - - - +
179B GLN* 1.4 62.3 + - - +
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Residues in contact with GLN 179 (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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80B VAL* 3.7 24.2 - - + +
81B ILE* 3.6 4.4 - - - -
82B PRO* 3.4 37.4 - - - +
83B VAL* 4.8 1.8 - - - -
109B MET* 6.1 0.6 - - - +
170B LEU* 3.7 4.0 - - - +
171B ARG* 2.9 36.3 + - + +
173B GLN* 3.4 43.3 + - + +
177B ILE* 4.8 5.9 - - - +
178B GLN* 1.4 75.7 + - - +
180B ALA* 1.3 60.4 + - - +
181B LYS 4.1 0.7 + - - -
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Residues in contact with ALA 180 (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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79B GLN 3.3 3.6 - - - +
80B VAL* 3.3 5.0 - - - -
81B ILE 2.8 39.1 + - - +
83B VAL* 4.0 13.2 - - + +
121B ALA* 4.4 5.8 - - + -
123B LEU* 4.6 3.6 - - + -
167B VAL* 5.1 0.2 - - + -
169B GLU 3.6 4.7 - - - +
170B LEU* 3.7 20.6 - - + -
179B GLN* 1.3 73.4 - - - +
181B LYS* 1.4 59.0 + - - +
182B VAL* 3.5 20.3 + - + +
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Residues in contact with LYS 181 (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 CYS* 3.8 26.7 - - - -
79B GLN 3.6 4.0 - - - -
80B VAL* 4.2 17.9 - - + +
167B VAL* 3.9 0.5 - - - -
168B LEU* 2.8 54.8 + - + +
169B GLU* 2.8 42.6 + - + +
179B GLN 4.1 0.8 + - - -
180B ALA* 1.4 67.8 - - - +
182B VAL* 1.3 56.7 + - - +
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Residues in contact with VAL 182 (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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77B SER 3.8 0.2 - - - +
78B CYS* 3.1 8.0 - - - +
79B GLN* 2.8 37.4 + - + +
81B ILE* 3.9 19.1 - - + -
121B ALA* 5.1 0.2 - - + -
165B PHE* 3.3 58.8 - - + -
166B LYS 3.4 5.4 - - - +
167B VAL* 4.5 2.7 - - - -
168B LEU* 3.9 4.5 - - - -
180B ALA* 3.8 20.6 - - + +
181B LYS* 1.3 79.0 - - - +
183B GLN* 1.3 60.3 + - - +
184B ILE* 4.0 11.2 - - + -
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Residues in contact with GLN 183 (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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76B ASP* 3.4 29.2 + - - +
77B SER 3.4 3.8 - - - +
78B CYS* 5.1 5.3 - - - +
165B PHE* 3.3 4.3 - - - -
166B LYS* 2.9 44.6 + - + +
168B LEU* 3.9 32.0 - - + +
182B VAL* 1.3 71.3 - - - +
184B ILE* 1.3 68.2 + - - +
185B LEU* 3.3 5.4 + - + +
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Residues in contact with ILE 184 (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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73B HIS* 3.8 33.7 - - + +
74B ASP 3.7 18.2 - - - +
75B ASP* 4.2 8.5 - - - +
76B ASP* 2.9 30.0 + - - -
77B SER* 3.0 18.2 + - - +
79B GLN* 4.3 5.8 - - + -
81B ILE* 4.8 0.4 - - + -
138B THR* 4.3 16.8 - - + -
163B GLN* 3.5 33.2 - - + +
164B ARG 3.8 5.6 - - - +
165B PHE* 4.4 4.0 - - + -
182B VAL* 4.0 20.2 - - + -
183B GLN* 1.3 69.1 - - - +
185B LEU* 1.3 67.3 + - - +
186B PRO* 3.7 1.6 - - - +
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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