Contacts of the strand formed by residues 114 - 121 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D GLN* 3.5 8.5 + - - +
62D LEU* 2.7 49.3 + - + +
76D TYR* 3.7 24.9 - - + +
112D LEU* 3.9 22.9 - - + -
113D ASN* 1.3 80.1 - - - +
115D THR* 1.3 76.4 + - - +
116D ARG* 3.8 17.3 - - + +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER* 3.7 17.9 - - - +
60D SER 3.5 12.1 - - - +
61D GLN* 2.7 24.7 + - + +
114D VAL* 1.3 84.8 - - - +
116D ARG* 1.3 67.5 + - - +
117D GLY 5.0 0.2 - - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER* 2.6 55.7 + - - +
62D LEU* 4.2 10.3 - - + +
76D TYR* 4.0 26.5 + - - -
77D TRP* 4.6 5.7 - - - +
78D LEU* 3.8 44.7 + - + +
90D ALA* 5.2 4.0 - - - +
91D LYS* 4.6 22.6 - - - +
114D VAL* 3.8 14.3 + - + +
115D THR* 1.3 82.4 - - - +
117D GLY* 1.3 62.3 + - - +
118D PHE* 4.7 1.9 - - - -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D TYR* 3.2 27.8 + - - -
58D ILE 3.3 9.6 - - - -
59D SER* 4.0 3.6 - - - -
90D ALA* 4.8 3.3 - - - +
91D LYS* 6.0 0.7 - - - -
115D THR* 4.4 1.8 - - - +
116D ARG* 1.3 82.9 + - - +
118D PHE* 1.3 65.1 + - - +
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ARG* 3.6 16.4 - - - +
46D LEU* 5.0 0.4 - - + -
57D TYR* 3.5 9.7 - - - -
58D ILE* 2.9 65.8 + - + -
60D SER* 4.6 8.3 - - - -
78D LEU* 4.4 9.9 - - + -
80D ILE* 3.8 20.2 - - + -
88D PHE* 5.0 0.2 - + - -
90D ALA* 3.6 26.5 - - + +
116D ARG 4.7 0.4 - - - -
117D GLY* 1.3 78.5 - - - +
119D TRP* 1.3 62.2 + - - +
120D VAL* 3.6 29.5 + - + -
131D VAL* 3.6 32.5 - - + -
149D PHE* 4.2 4.9 - + - -
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Residues in contact with TRP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ARG* 2.9 33.3 + - - +
54D ASN 5.9 1.1 - - - -
55D GLY 5.2 1.1 - - - -
56D GLY* 3.4 36.6 - - - -
57D TYR* 3.8 33.0 - + + -
118D PHE* 1.3 75.0 - - - +
120D VAL* 1.3 69.3 + - - +
121D PRO* 3.7 15.5 - - + -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ARG* 4.7 0.2 - - - +
51D LEU* 3.7 19.3 - - + -
55D GLY* 3.2 2.3 - - - -
56D GLY 2.9 32.1 + - - +
58D ILE* 4.4 1.6 - - + -
88D PHE* 4.6 8.1 - - + -
118D PHE* 3.6 28.0 - - + +
119D TRP* 1.3 77.7 - - - +
121D PRO* 1.3 67.1 - - - +
124D MET* 4.4 11.4 - - + -
129D TYR* 4.8 6.1 - - + -
149D PHE* 3.8 23.1 - - + -
151D LYS* 3.9 24.2 - - + -
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Residues in contact with PRO 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLU* 4.1 6.1 - - - +
219C ARG* 3.8 12.8 - - - +
221C LYS* 6.1 0.7 - - - +
55D GLY* 4.2 0.7 - - - -
119D TRP* 3.7 21.5 - - + +
120D VAL* 1.3 91.9 - - - +
122D GLU* 1.3 67.3 + - - +
123D TYR* 3.2 46.0 - - + +
124D MET* 3.1 31.4 + - + +
151D LYS* 3.4 5.0 - - - -
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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