Contacts of the strand formed by residues 24 - 33 (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 MET 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A HIS 3.0 15.1 + - - +
23A HIS* 1.3 93.5 + - - +
25A GLY* 1.3 58.4 + - - +
98A PRO* 3.4 20.8 - - + +
128A PRO 4.4 1.0 + - - -
130A ILE* 3.9 16.3 - - + +
135A ALA* 3.8 21.8 - - + -
138A MET* 5.6 1.6 - - + -
139A ILE* 3.3 42.0 - - + -
199A ILE* 3.8 13.7 - - + -
200A GLY* 3.6 1.3 - - - -
201A ASP* 3.5 24.9 - - - -
209A LEU* 3.4 29.2 - - + +
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Residues in contact with GLY 25 (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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23A HIS 3.8 1.2 + - - -
24A MET* 1.3 74.9 - - - +
26A ILE* 1.3 60.3 + - - -
98A PRO* 3.7 9.4 - - - -
118A SER* 3.0 18.8 - - - -
167A SER* 5.5 0.7 - - - -
169A ILE* 5.5 1.6 - - - +
198A ARG 3.9 1.6 - - - +
199A ILE* 3.3 7.1 - - - +
200A GLY 3.3 31.0 + - - +
202A MET* 3.7 13.4 - - - +
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Residues in contact with ILE 26 (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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25A GLY* 1.3 74.4 - - - -
27A ASP* 1.3 69.2 + - - +
28A VAL* 4.8 5.2 - - + +
92A PHE* 6.0 1.8 - - + -
94A PHE* 6.4 0.7 - - + -
97A CYS* 4.9 7.2 - - + -
98A PRO* 3.5 37.9 - - + +
99A GLN 4.5 0.7 - - - +
100A ILE* 3.7 25.4 - - + -
116A LEU 5.5 0.4 - - - +
117A SER* 3.0 4.4 - - - -
118A SER* 2.9 33.7 + - - +
142A CYS* 4.9 12.8 - - - -
144A VAL* 5.3 7.6 - - + -
167A SER* 4.3 0.9 + - - -
179A ILE* 5.3 0.7 - - + -
197A VAL* 3.4 33.7 - - + -
198A ARG 4.2 2.0 - - - +
199A ILE* 4.3 16.6 - - + -
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Residues in contact with ASP 27 (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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26A ILE* 1.3 83.9 - - - +
28A VAL* 1.3 70.1 + - - +
29A ILE* 4.3 2.8 + - - +
115A ARG* 3.6 19.4 + - - +
116A LEU 3.5 4.7 - - - -
117A SER* 3.3 13.2 + - - -
166A GLY* 5.6 0.5 - - - -
167A SER* 2.6 25.8 + - - +
169A ILE* 3.7 14.0 - - + +
171A HIS* 4.0 24.7 + - + -
196A SER 3.9 0.9 - - - +
197A VAL* 3.7 3.2 - - - -
198A ARG* 3.5 26.9 + - + +
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Residues in contact with VAL 28 (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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26A ILE* 4.8 4.4 - - + +
27A ASP* 1.3 78.4 - - - +
29A ILE* 1.3 75.9 + - - +
30A ILE* 4.0 13.2 - - + -
92A PHE* 3.7 31.0 - - + -
100A ILE* 5.8 0.7 - - + -
114A ALA 4.0 0.3 - - - +
115A ARG* 3.7 6.2 - - - -
116A LEU* 2.9 50.6 + - + +
144A VAL* 5.7 1.6 - - + -
146A ILE* 5.6 6.1 - - + -
195A PHE* 5.6 2.0 - - + -
196A SER 3.3 12.6 - - - +
197A VAL* 4.0 18.6 - - + +
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Residues in contact with ILE 29 (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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27A ASP* 4.5 6.1 - - - +
28A VAL* 1.3 81.1 - - - +
30A ILE* 1.3 73.7 + - - +
31A LYS 4.3 0.4 - - - +
114A ALA 4.2 2.0 - - - -
115A ARG* 4.4 9.2 - - - +
171A HIS* 3.4 38.1 - - + +
194A GLU 4.6 0.4 - - - -
195A PHE* 3.6 5.9 - - - +
196A SER* 2.7 48.8 + - - +
229A ASP* 3.6 15.0 - - + +
232A LEU* 4.5 11.9 - - + -
233A ILE* 3.4 40.4 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.0 18.4 - - + -
29A ILE* 1.3 88.7 - - - +
31A LYS* 1.3 58.4 + - - +
32A VAL* 3.7 14.7 + - + +
83A ILE* 5.4 2.2 - - + -
90A MET* 5.2 16.8 - - + -
92A PHE* 4.8 16.4 - - + -
112A VAL 3.8 0.5 - - - +
113A ASN* 3.3 9.1 - - - +
114A ALA* 3.3 48.9 + - + +
116A LEU* 5.2 5.6 - - + -
146A ILE* 5.4 15.7 - - + -
193A LEU* 3.7 26.9 - - + -
194A GLU 3.7 3.1 - - - +
195A PHE* 5.5 2.9 - - + -
233A ILE* 5.2 0.2 - - - -
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Residues in contact with LYS 31 (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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29A ILE* 4.3 1.0 - - - +
30A ILE* 1.3 69.9 - - - +
32A VAL* 1.3 62.7 + - - +
33A THR* 4.2 15.6 + - - +
108A ASP* 5.7 3.4 - - - -
111A THR* 4.2 20.3 + - - +
113A ASN* 3.7 16.4 - - - +
192A ASN 3.7 1.9 - - - +
193A LEU* 3.5 4.1 + - - -
194A GLU* 3.2 48.8 + - + +
232A LEU* 3.5 45.9 - - + +
233A ILE* 4.0 7.4 - - + -
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Residues in contact with VAL 32 (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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30A ILE* 3.8 24.7 - - + +
31A LYS* 1.3 73.9 - - - +
33A THR* 1.3 64.5 + - - +
88A LEU* 3.7 15.7 - - + -
90A MET* 4.3 13.7 - - + -
111A THR* 3.2 7.7 - - - -
112A VAL* 2.9 47.3 + - + +
113A ASN 5.9 0.2 - - - -
114A ALA* 6.1 0.4 - - + -
148A ILE* 3.6 25.1 - - + -
190A VAL* 3.6 24.2 - - + -
192A ASN 3.8 2.2 - - - -
193A LEU* 4.2 8.1 - - + -
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Residues in contact with THR 33 (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* 4.2 17.2 + - - -
32A VAL* 1.3 76.0 + - - +
34A LYS* 1.3 66.7 + - - +
110A ASN* 3.7 20.9 - - - +
111A THR* 4.3 6.5 - - + +
190A VAL* 3.4 6.4 - - - -
191A LYS* 2.8 32.3 + - + -
192A ASN* 2.7 49.5 + - - +
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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