Contacts of the strand formed by residues 114 - 121 (chain A) in PDB entry 4BEI
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 VAL 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.5 8.0 + - - +
62A LEU* 2.7 50.7 + - + +
64A ILE* 6.5 0.2 - - + -
76A TYR* 3.7 23.8 - - + +
112A LEU* 3.9 22.4 - - + -
113A ASN* 1.3 78.8 - - - +
115A THR* 1.3 76.7 + - - +
116A ARG* 3.8 16.8 - - + +
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Residues in contact with THR 115 (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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59A SER* 3.7 17.3 - - - +
60A SER 3.5 12.8 - - - +
61A GLN* 2.7 24.7 + - + +
114A VAL* 1.3 83.8 - - - +
116A ARG* 1.3 65.4 + - - +
117A GLY 5.0 1.1 - - - +
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Residues in contact with ARG 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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58A ILE 4.3 0.2 - - - +
60A SER* 2.6 55.5 + - - +
62A LEU* 4.2 9.0 - - + -
76A TYR* 4.0 25.5 + - - -
77A TRP* 4.6 6.1 - - - +
78A LEU* 3.8 46.7 + - + +
90A ALA* 5.2 3.8 - - - +
91A LYS* 4.6 25.3 - - - +
114A VAL* 3.8 13.8 + - + +
115A THR* 1.3 82.2 - - - +
117A GLY* 1.3 60.5 + - - +
118A PHE* 4.7 2.1 - - - -
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Residues in contact with GLY 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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57A TYR* 3.2 27.4 + - - -
58A ILE 3.3 9.4 - - - -
59A SER* 4.0 4.0 - - - -
78A LEU* 6.2 0.2 - - - -
90A ALA* 4.8 4.0 - - - +
91A LYS* 6.0 0.5 - - - -
115A THR* 5.0 1.8 - - - +
116A ARG* 1.3 80.6 + - - +
118A PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 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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46A LEU* 5.0 0.2 - - + -
57A TYR* 3.5 9.7 - - - -
58A ILE* 2.9 64.0 + - + -
60A SER* 4.6 8.3 - - - -
78A LEU* 4.4 10.3 - - + -
80A ILE* 3.8 20.9 - - + -
88A PHE* 5.0 0.7 - + - -
90A ALA* 3.6 37.9 - - + +
116A ARG 4.7 0.7 - - - -
117A GLY* 1.3 79.6 - - - +
119A TRP* 1.3 64.3 + - - +
120A VAL* 3.6 28.6 + - + +
131A VAL* 3.6 33.4 - - + -
149A PHE* 4.2 4.9 - + - -
219B ARG* 4.2 2.0 - - - +
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Residues in contact with TRP 119 (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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54A ASN 5.9 1.3 - - - -
55A GLY 5.1 0.4 - - - -
56A GLY* 3.4 36.6 - - - -
57A TYR* 3.8 31.7 - + + -
88A PHE* 4.6 0.7 - - - -
118A PHE* 1.3 75.5 - - - +
120A VAL* 1.3 67.0 + - - +
121A PRO* 4.5 12.1 - - + -
219B ARG* 2.6 37.8 + - - +
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Residues in contact with VAL 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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51A LEU* 3.7 18.8 - - + -
55A GLY* 3.2 2.3 - - - -
56A GLY 2.9 32.3 + - - +
58A ILE* 4.4 0.9 - - + -
88A PHE* 4.6 8.5 - - + -
118A PHE* 3.6 28.0 - - + +
119A TRP* 1.3 78.2 - - - +
121A PRO* 1.3 67.1 - - - +
124A MET* 4.4 11.2 - - + -
129A TYR* 4.8 6.7 - - + -
149A PHE* 3.9 23.3 - - + -
151A LYS* 3.9 25.1 - - + -
219B ARG* 4.5 0.4 - - - +
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Residues in contact with PRO 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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55A GLY* 4.8 0.2 - - - -
119A TRP* 3.7 14.4 - - + +
120A VAL* 1.3 89.8 - - - +
122A GLU* 1.3 67.8 + - - +
123A TYR* 3.3 47.3 - - + +
124A MET* 3.1 31.2 + - + +
151A LYS* 3.4 4.7 - - - -
201B GLU* 4.1 3.8 - - - +
219B ARG* 3.5 22.9 - - - +
221B LYS* 6.1 0.7 - - - +
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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