Contacts of the strand formed by residues 114 - 120 (chain A) in PDB entry 5J3S
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 PHE 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 1.3 81.0 - - - +
115A SER* 1.3 82.5 + - - +
116A LEU* 5.5 3.8 - - + -
146A ASP* 3.6 15.5 - - + -
147A VAL* 3.6 29.2 - - + -
188A ARG* 5.6 2.5 - - - +
213A VAL* 6.2 0.2 - - + -
215A VAL* 4.7 27.4 - - + -
220A LEU* 6.2 2.0 - - + -
222A LEU* 4.3 10.3 - - + -
258A ILE* 3.7 27.6 - - + -
355A ASN* 3.4 5.4 - - - +
356A LEU* 2.7 60.9 + - + +
357A ASP* 4.5 3.1 - - - +
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Residues in contact with SER 115 (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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114A PHE* 1.3 94.2 - - - +
116A LEU* 1.3 65.2 + - - +
144A SER 4.7 1.4 + - - -
145A PRO* 3.5 12.5 - - - +
146A ASP* 3.2 21.4 + - - +
147A VAL 3.4 17.2 + - - -
188A ARG* 5.7 2.1 + - - -
353A LEU* 4.4 7.4 - - - -
354A CYS 3.4 9.9 - - - -
355A ASN* 4.2 15.0 - - - -
356A LEU* 4.9 1.3 - - - -
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Residues in contact with LEU 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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114A PHE* 5.5 3.6 - - + -
115A SER* 1.3 77.8 - - - +
117A ILE* 1.3 67.2 + - - +
118A THR* 4.2 12.3 - - - +
145A PRO* 4.6 1.1 - - - -
147A VAL* 3.1 15.9 - - + +
149A PHE* 3.7 23.6 - - + -
222A LEU* 5.7 1.1 - - + -
258A ILE* 3.5 34.5 - - + -
260A ALA* 4.7 1.1 - - + -
318A ILE* 3.7 35.0 - - + -
352A LEU 5.0 0.4 - - - +
353A LEU* 3.2 9.2 - - - +
354A CYS* 3.1 44.1 + - + +
356A LEU* 4.9 6.5 - - + -
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Residues in contact with ILE 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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116A LEU* 1.3 81.5 - - - +
118A THR* 1.3 63.9 + - - +
119A TRP* 4.1 12.3 + - + -
140A LEU* 3.7 34.1 - - + -
143A TYR* 4.5 10.5 - - + -
145A PRO* 3.8 19.5 - - + -
147A VAL 3.1 9.4 + - - +
148A ILE* 3.5 6.9 - - + +
149A PHE* 2.8 32.7 + - - +
150A LEU* 6.1 0.2 - - + -
335A LEU* 3.7 27.4 - - + -
352A LEU 3.1 14.4 - - - +
353A LEU* 3.7 17.7 - - + -
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Residues in contact with THR 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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116A LEU* 4.2 5.3 - - - +
117A ILE* 1.3 71.8 - - - +
119A TRP* 1.3 67.2 + - - +
149A PHE* 3.4 9.4 - - - +
151A GLN* 3.9 5.8 - - - +
260A ALA* 3.1 27.7 - - - +
261A GLY* 3.6 29.2 - - - +
316A ASP* 3.8 23.9 - - + +
317A ARG 5.1 1.1 - - - +
318A ILE* 4.4 4.3 - - - +
350A TRP 4.2 1.2 - - - +
351A GLY* 3.4 0.5 - - - -
352A LEU* 2.7 48.4 + - - +
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Residues in contact with TRP 119 (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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117A ILE* 4.5 9.9 - - + -
118A THR* 1.3 77.3 - - - +
120A ASN* 1.3 75.2 + - - +
121A ILE* 3.3 11.1 + - + -
136A VAL* 4.3 23.1 - - + -
139A TYR* 4.1 31.6 - + + -
140A LEU* 5.3 3.8 - - + -
149A PHE 3.0 7.1 + - - -
150A LEU* 3.4 21.4 - - + +
151A GLN* 3.3 20.3 + - - -
316A ASP* 4.7 0.4 - - - -
335A LEU* 4.1 14.6 - - + -
336A GLY* 3.7 35.7 - - - -
346A PRO* 3.9 22.4 - - + -
347A SER* 3.4 11.7 - - - -
349A HIS 3.2 19.5 + - - -
350A TRP 3.8 5.8 - - - -
351A GLY* 3.5 23.4 - - - +
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Residues in contact with ASN 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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119A TRP* 1.3 74.1 - - - +
121A ILE* 1.3 49.9 - - - +
122A ASP* 3.0 7.6 + - - -
151A GLN* 3.2 19.0 + - + +
152A GLU* 3.1 45.4 + - - +
226A HIS* 3.9 6.2 - - - -
262A ASP* 3.5 12.1 + - + -
316A ASP* 4.0 6.2 + - - +
347A SER* 2.2 31.2 + - - -
348A ASP* 4.0 2.4 + - - +
349A HIS* 3.2 49.1 + - + +
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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