Contacts of the strand formed by residues 114 - 119 (chain B) in PDB entry 2FHP
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 PHE 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B MSE 3.5 26.2 - - + +
45B ALA 3.8 16.6 - - - -
46B LEU* 3.7 23.6 - - + -
68B ILE* 3.8 24.0 - - + -
107B PHE* 3.6 43.1 - + + -
112B LEU* 4.0 16.4 - - + -
113B GLN* 1.3 74.5 - - - +
115B ASP* 1.3 59.4 + - - +
116B LEU 3.9 10.1 - - - +
117B VAL* 4.0 10.5 - - + -
135B MSE 3.9 13.0 - - + -
140B LEU* 2.9 21.7 + - + +
141B LEU* 3.6 2.6 - - - +
142B THR* 3.0 23.9 + - - -
145B ALA* 3.5 9.2 - - - +
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Residues in contact with ASP 115 (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 GLY 5.4 0.7 - - - +
43B GLY* 3.3 11.0 - - - -
44B MSE 2.8 34.6 + - - +
64B MSE 4.2 8.7 - - + -
113B GLN 4.7 1.0 - - - +
114B PHE* 1.3 73.8 - - - +
116B LEU* 1.3 59.0 + - - +
142B THR* 2.9 35.4 + - - +
144B GLU* 4.4 12.6 - - - +
145B ALA* 3.3 3.3 - - - +
146B VAL* 3.0 30.1 + - - +
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Residues in contact with LEU 116 (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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33B PHE* 4.1 15.0 - - + -
36B ILE* 3.7 17.5 - - + -
40B PHE* 4.6 2.2 - - + -
44B MSE 3.3 3.0 + - - +
45B ALA* 3.2 6.8 - - + -
46B LEU 2.8 25.6 + - - -
59B ALA* 3.8 19.5 - - + -
64B MSE 3.5 33.0 - - - -
114B PHE* 3.9 1.4 - - - +
115B ASP* 1.3 81.1 - - - +
117B VAL* 1.3 70.3 + - - +
118B LEU* 4.2 14.8 - - + -
146B VAL* 3.3 31.0 - - + +
148B VAL* 4.0 13.7 - - + -
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Residues in contact with VAL 117 (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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46B LEU* 3.5 15.7 - - + +
114B PHE* 4.0 8.3 - - + -
116B LEU* 1.3 81.0 - - - +
118B LEU* 1.3 58.6 + - - +
119B LEU* 3.7 31.0 - - + -
135B MSE 3.8 26.0 - - + -
141B LEU* 3.7 29.8 - - + -
145B ALA* 5.9 0.4 - - + -
146B VAL 3.0 7.3 + - - +
147B ILE* 3.4 14.6 - - + +
148B VAL* 2.8 32.4 + - - +
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Residues in contact with LEU 118 (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 ILE* 5.0 0.7 - - + -
33B PHE* 4.1 18.4 - - + -
45B ALA* 4.9 2.7 - - + -
46B LEU 2.8 20.0 + - - +
47B ASP* 3.8 17.9 - - + +
48B LEU 3.1 24.4 + - - -
55B LEU* 3.9 49.6 - - + +
56B ALA* 4.2 5.6 - - - +
59B ALA* 4.8 2.0 - - + -
116B LEU* 4.2 20.9 - - + -
117B VAL* 1.3 72.5 - - - +
119B LEU* 1.3 64.1 + - - +
120B ASP* 4.0 3.0 + - - -
148B VAL* 3.6 29.8 - - + -
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Residues in contact with LEU 119 (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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48B LEU* 3.7 30.7 - - + -
49B TYR* 4.7 3.1 - - + -
55B LEU* 5.9 0.4 - - - +
117B VAL* 3.7 20.6 - - + -
118B LEU* 1.3 80.3 - - - +
120B ASP* 1.3 59.8 + - - +
121B PRO* 3.3 9.0 - - + +
128B ILE* 4.1 35.3 - - + +
131B GLN* 4.5 10.8 - - + +
132B LEU* 4.0 17.7 - - + -
135B MSE 5.7 1.8 - - - -
147B ILE* 3.9 20.6 - - + -
148B VAL* 2.8 15.4 + - - +
149B CYS* 3.5 2.5 - - - -
150B GLU* 2.8 27.2 + - - -
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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