Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 2FIN
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE* 3.6 4.9 - - - +
101A LYS* 1.3 78.6 - - - +
103A ILE* 1.3 61.0 + - - +
104A SER* 5.2 0.2 - - - -
115A ARG* 4.2 3.0 + - - +
116A LEU* 3.4 6.6 - - - -
117A SER* 2.4 58.4 + - - +
118A SER 4.6 4.3 - - - -
119A VAL* 4.7 0.6 - - - +
164A VAL* 5.2 3.4 - - - -
165A LEU* 3.2 37.2 + - - -
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Residues in contact with ILE 103 (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 VAL* 4.8 12.1 - - + -
83A ILE* 3.4 33.2 - - + -
100A ILE* 6.1 0.4 - - + -
101A LYS 4.1 6.3 + - - +
102A SER* 1.3 74.8 - - - +
104A SER* 1.3 77.7 + - - +
105A GLU* 4.5 5.4 - - + +
115A ARG 3.7 1.3 - - - -
116A LEU* 3.5 24.9 - - + -
240A ALA* 3.3 6.5 - - + +
241A CYS* 3.2 27.7 + - + -
242A VAL* 4.5 19.7 - - - +
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Residues in contact with SER 104 (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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103A ILE* 1.3 80.6 + - - +
105A GLU* 1.3 73.4 + - - +
114A ALA* 3.5 0.2 - - - -
115A ARG* 3.0 29.9 + - - +
164A VAL* 2.9 34.6 - - - +
238A LEU* 3.8 12.1 - - - -
239A LYS 3.1 21.1 - - - -
240A ALA* 3.4 11.3 + - - +
241A CYS* 4.0 1.8 - - - -
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Residues in contact with GLU 105 (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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44A ILE* 3.9 18.2 - - + +
45A CYS* 3.8 13.1 + - - -
47A SER 5.2 0.9 - - - +
83A ILE* 3.7 27.7 - - - +
84A ILE 4.0 10.3 - - - +
85A GLY* 4.4 7.6 - - - -
90A MET* 4.4 15.9 - - - +
103A ILE* 4.5 3.6 - - + -
104A SER* 1.3 86.9 - - - +
106A SER* 1.3 62.6 + - - +
112A VAL* 6.0 0.9 - - - +
113A ASN 3.6 17.1 - - - +
114A ALA* 4.1 9.4 - - + +
238A LEU* 3.9 5.4 - - - -
239A LYS* 2.9 33.5 + - - +
241A CYS* 3.5 23.1 - - - +
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Residues in contact with SER 106 (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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44A ILE* 3.7 12.2 - - - +
105A GLU* 1.3 75.1 - - - +
107A ALA* 1.3 66.4 + - - +
108A ASP* 5.0 2.4 - - - +
112A VAL* 3.4 6.9 - - - +
113A ASN* 3.0 37.0 + - - +
237A LYS* 2.7 48.2 + - - +
238A LEU* 4.3 8.3 - - - -
239A LYS* 5.5 2.8 - - - +
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Residues in contact with ALA 107 (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 ASP* 3.6 35.2 - - + +
44A ILE* 3.7 19.1 - - + +
106A SER* 1.3 81.5 + - - +
108A ASP* 1.3 62.5 + - - +
109A GLY 4.3 2.0 - - - +
111A THR 3.8 4.7 - - - +
112A VAL* 4.1 7.9 - - + -
237A LYS* 5.5 3.6 - - - -
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Residues in contact with ASP 108 (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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31A LYS* 5.7 3.5 - - - -
106A SER* 5.7 1.1 - - - +
107A ALA* 1.3 76.5 - - - +
109A GLY* 1.3 65.0 + - - +
110A ASN 3.5 0.3 + - - -
111A THR* 2.8 42.1 + - - +
113A ASN* 3.7 22.4 + - - -
237A LYS* 5.2 14.1 - - + +
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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