Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 2F5O
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 THR 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.4 6.7 - - - -
35A ARG* 3.8 41.5 - - + +
61A PHE* 4.9 4.3 - - - -
72A ILE 4.4 0.8 + - - -
73A SER* 3.4 3.8 + - - -
74A HIS* 3.0 44.7 + - - +
76A ARG* 4.1 18.2 + - - +
108A TYR* 5.5 0.7 - - - -
114A PHE 3.9 5.8 - - - +
115A GLY* 1.3 80.4 - - - +
117A MET* 1.3 69.0 + - - +
118A HIS* 4.2 12.9 + - + -
130A PRO* 5.5 0.3 - - - +
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Residues in contact with MET 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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33A ILE* 3.0 16.8 + - + +
34A ILE* 3.8 4.9 - - - -
35A ARG 2.8 26.3 + - - -
36A HIS 3.6 1.6 + - - +
43A PHE* 3.9 32.7 - - + -
71A LEU* 4.0 11.7 - - + -
72A ILE 3.4 4.9 - - - -
73A SER* 4.4 4.5 - - - +
81A TYR* 3.6 17.3 - - - +
96A VAL* 3.8 24.0 - - + -
98A PHE* 3.9 14.8 - - + -
108A TYR* 3.6 41.7 - - + -
116A THR* 1.3 79.8 - - - +
118A HIS* 1.3 64.2 + - - +
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.3 37.2 - - + +
36A HIS* 3.5 12.8 - - + -
71A LEU* 3.5 2.4 - - - +
72A ILE* 2.7 39.7 + - + +
116A THR* 4.2 12.6 + - + -
117A MET* 1.3 78.2 + - - +
119A VAL* 1.3 61.0 + - - +
120A TYR* 3.8 26.0 - - + -
129A PRO* 3.7 21.1 + - + +
130A PRO* 3.6 35.9 - - + +
11C C 5.6 2.8 + - - -
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Residues in contact with VAL 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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36A HIS* 2.8 45.2 + - - +
37A PRO* 3.9 6.0 - - + +
43A PHE* 3.1 34.1 - - + -
46A ARG* 3.7 28.3 + - - +
47A MET* 3.8 31.0 - - + -
69A ASP* 3.9 7.6 - - + -
70A ALA 3.4 9.2 - - - +
71A LEU* 3.9 12.6 - - + -
118A HIS* 1.3 76.7 - - - +
120A TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 120 (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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36A HIS* 3.2 49.9 - + - +
46A ARG* 4.3 4.0 - - - +
69A ASP* 3.3 8.0 - - - -
70A ALA* 2.8 27.0 + - - +
72A ILE* 4.3 10.5 - - + -
118A HIS* 3.8 21.7 - - + -
119A VAL* 1.3 74.6 - - - +
121A ALA* 1.3 73.4 + - - +
124A GLU* 4.0 13.7 - - + -
125A ALA* 4.2 15.9 - - + +
128A ARG* 3.7 33.2 - - + -
129A PRO* 3.0 44.0 + - - +
130A PRO* 4.9 0.2 - - + -
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Residues in contact with ALA 121 (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 ARG* 3.9 4.9 - - - +
68A ARG* 3.7 24.7 - - + +
69A ASP* 3.2 14.5 + - - +
120A TYR* 1.3 76.0 - - - +
122A LYS* 1.3 66.1 + - - +
123A GLU* 3.7 24.0 - - - +
124A GLU* 3.0 27.9 + - - +
125A ALA* 3.3 7.3 + - - +
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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