Contacts of the strand formed by residues 114 - 121 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61H GLN* 3.5 7.5 + - - +
62H LEU* 2.7 49.9 + - + +
64H ILE* 6.5 0.2 - - + -
76H TYR* 3.7 24.7 - - + +
112H LEU* 3.9 22.0 - - + -
113H ASN* 1.3 80.5 - - - +
115H THR* 1.3 76.9 + - - +
116H ARG* 3.8 16.8 - - + +
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Residues in contact with THR 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H SER* 3.7 16.8 - - - +
60H SER 3.5 12.1 - - - +
61H GLN* 2.7 24.8 + - + +
114H VAL* 1.3 84.2 - - - +
116H ARG* 1.3 65.7 + - - +
117H GLY 5.0 0.9 - - - +
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Residues in contact with ARG 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H ILE 4.3 0.2 - - - +
60H SER* 2.6 55.2 + - - +
62H LEU* 4.2 10.1 - - + -
76H TYR* 4.0 26.3 + - - -
77H TRP* 4.6 6.3 - - - +
78H LEU* 3.8 44.6 + - + +
90H ALA* 5.2 3.8 - - - +
91H LYS* 4.6 22.0 - - - +
114H VAL* 3.8 13.2 + - + +
115H THR* 1.3 81.4 - - - +
117H GLY* 1.3 60.5 + - - +
118H PHE* 4.7 1.7 - - - -
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Residues in contact with GLY 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H TYR* 3.2 27.1 + - - -
58H ILE 3.3 9.2 - - - -
59H SER* 4.0 4.3 - - - -
90H ALA* 4.8 4.2 - - - +
91H LYS* 6.0 0.3 - - - -
115H THR* 5.0 2.0 - - - +
116H ARG* 1.3 82.6 + - - +
118H PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G ARG* 4.2 0.4 - - - +
46H LEU* 5.0 0.2 - - + -
57H TYR* 3.5 10.0 - - - -
58H ILE* 2.9 65.9 + - + +
60H SER* 4.6 8.3 - - - -
78H LEU* 4.4 10.1 - - + -
80H ILE* 3.8 21.3 - - + -
88H PHE* 5.0 1.1 - + - -
90H ALA* 3.6 38.1 - - + +
116H ARG 4.7 0.7 - - - -
117H GLY* 1.3 79.0 - - - +
119H TRP* 1.3 64.8 + - - +
120H VAL* 3.6 28.2 + - + -
131H VAL* 3.6 33.4 - - + -
149H PHE* 4.2 4.7 - + - -
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Residues in contact with TRP 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G ARG* 2.7 38.2 + - - +
54H ASN 5.9 1.1 - - - -
55H GLY 5.2 0.7 - - - -
56H GLY* 3.4 37.2 - - - -
57H TYR* 3.8 32.8 - + + -
88H PHE* 4.6 0.7 - - - -
118H PHE* 1.3 76.9 - - - +
120H VAL* 1.3 67.7 + - - +
121H PRO* 4.5 12.1 - - + -
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Residues in contact with VAL 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G ARG* 4.5 0.2 - - - +
51H LEU* 3.7 18.6 - - + -
55H GLY* 3.2 2.3 - - - -
56H GLY 2.9 32.7 + - - +
58H ILE* 4.4 1.6 - - + -
88H PHE* 4.6 8.1 - - + -
118H PHE* 3.6 27.4 - - + +
119H TRP* 1.3 77.8 - - - +
121H PRO* 1.3 65.5 - - - +
124H MET* 4.4 11.7 - - + -
129H TYR* 4.8 6.7 - - + -
149H PHE* 3.8 23.6 - - + -
151H LYS* 3.9 24.2 - - + -
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Residues in contact with PRO 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G GLU* 4.1 3.4 - - - +
219G ARG* 3.5 22.2 - - - +
221G LYS* 6.1 1.1 - - - +
54H ASN 5.3 0.2 - - - +
55H GLY* 4.2 1.1 - - - -
119H TRP* 3.7 14.4 - - + -
120H VAL* 1.3 92.2 - - - +
122H GLU* 1.3 63.8 + - - +
123H TYR* 3.2 47.6 - - + +
124H MET* 3.1 32.3 + - + +
151H LYS* 3.4 4.9 - - - -
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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