Contacts of the strand formed by residues 114 - 119 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A MSE 3.6 25.8 - - + +
45A ALA 3.7 11.9 - - - -
46A LEU* 3.6 30.1 - - + -
68A ILE* 3.9 21.8 - - + -
107A PHE* 3.5 48.5 - + + -
112A LEU* 4.1 12.1 - - + -
113A GLN* 1.3 75.3 - - - +
115A ASP* 1.3 59.7 + - - +
116A LEU 3.9 10.8 - - - +
117A VAL* 4.1 9.4 - - + -
135A MSE 3.8 13.0 - - + -
140A LEU* 2.8 22.0 + - + +
141A LEU* 3.6 2.8 - - - +
142A THR* 3.0 23.6 + - - -
145A ALA* 3.4 9.5 - - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 5.4 0.4 - - - +
43A GLY* 3.2 12.5 - - - -
44A MSE 2.8 33.2 + - - +
64A MSE 4.0 18.6 - - + +
113A GLN 4.7 1.0 - - - +
114A PHE* 1.3 73.1 - - - +
116A LEU* 1.3 59.6 + - - +
142A THR* 3.0 34.5 + - - +
144A GLU* 4.3 3.7 - - - +
145A ALA* 3.4 6.2 - - - +
146A VAL* 3.1 24.8 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.9 15.9 - - + -
36A ILE* 3.6 25.6 - - + -
40A PHE* 4.9 0.7 - - + -
44A MSE 3.4 2.2 + - - -
45A ALA* 3.3 4.6 - - + -
46A LEU 2.8 25.1 + - - -
59A ALA* 3.9 28.7 - - + -
64A MSE 3.8 24.0 - - + -
114A PHE* 3.5 2.8 - - - +
115A ASP* 1.3 82.0 - - - +
117A VAL* 1.3 74.6 + - - +
118A LEU* 3.9 18.8 - - + -
146A VAL* 3.3 17.0 - - + +
148A VAL* 3.9 15.5 - - + -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.5 14.4 - - + -
114A PHE* 4.1 7.2 - - + -
115A ASP 5.7 0.4 - - - -
116A LEU* 1.3 80.8 - - - +
118A LEU* 1.3 60.4 + - - +
119A LEU* 3.5 31.9 - - + -
135A MSE 3.7 37.9 - - + -
141A LEU* 3.7 18.8 - - + -
146A VAL 3.0 6.3 + - - +
147A ILE* 3.4 15.8 - - + +
148A VAL* 2.8 33.4 + - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.9 1.6 - - + -
33A PHE* 4.1 18.8 - - + -
45A ALA* 4.8 4.5 - - + -
46A LEU 2.8 20.6 + - - +
47A ASP* 3.9 20.0 - - + +
48A LEU* 3.2 24.4 + - - +
55A LEU* 3.9 45.5 - - + +
56A ALA* 4.4 2.9 - - - +
116A LEU* 3.9 25.8 - - + -
117A VAL* 1.3 75.6 - - - +
119A LEU* 1.3 64.1 + - - +
120A ASP* 4.0 3.0 + - - -
148A VAL* 3.5 27.1 - - + -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.7 30.7 - - + -
49A TYR* 4.7 3.8 - - + -
55A LEU* 6.0 0.4 - - - +
117A VAL* 3.5 20.6 - - + -
118A LEU* 1.3 81.3 - - - +
120A ASP* 1.3 58.3 + - - +
121A PRO* 3.3 10.0 - - + +
128A ILE* 4.1 29.6 - - + +
131A GLN* 4.5 10.8 - - + +
132A LEU* 3.9 22.2 - - + -
135A MSE 5.5 1.6 - - - -
147A ILE* 3.9 21.5 - - + -
148A VAL 2.8 14.3 + - - +
149A CYS* 3.4 4.7 - - - +
150A GLU* 2.9 26.7 + - - +
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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