Contacts of the strand formed by residues 61 - 67 (chain A) in PDB entry 4EWE
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.8 14.1 - - + -
58A HIS* 3.5 24.7 - + + -
59A ARG 3.2 17.3 - - - -
60A GLY* 1.3 80.7 - - - +
62A GLU* 1.3 81.5 + - - +
63A THR* 3.8 5.8 - - + -
95A ALA* 2.9 30.1 + - - +
96A GLY 3.7 1.6 + - - -
117A TRP* 3.4 46.2 - + + -
118A VAL 3.4 12.1 - - - +
119A ASN* 4.0 4.0 - - - +
120A LEU* 3.8 9.6 - - - +
255A PRO 3.2 27.4 - - - -
257A VAL* 3.7 22.4 - - + -
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Residues in contact with GLU 62 (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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61A PHE* 1.3 82.6 - - - +
63A THR* 1.3 63.7 + - - +
64A VAL* 5.0 0.7 - - + -
92A TRP* 2.9 35.6 + - + +
93A MET 3.1 11.4 - - - +
94A THR* 2.7 32.6 + - - +
117A TRP* 3.3 6.1 - - - -
118A VAL* 2.8 56.4 + - + +
120A LEU* 3.8 21.7 - - + +
164A TYR 5.2 0.3 - - - +
165A THR* 5.3 0.2 - - - -
166A ARG* 3.9 16.8 + - - +
167A THR 4.8 6.1 + - - +
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Residues in contact with THR 63 (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 HIS* 3.9 19.0 + - + +
61A PHE* 3.8 13.7 - - + +
62A GLU* 1.3 77.1 - - - +
64A VAL* 1.3 61.1 + - - +
65A SER* 4.0 2.2 + - - -
91A GLN* 3.6 4.3 + - - +
92A TRP* 3.8 0.3 - - - -
93A MET* 2.8 58.5 + - + +
101A HIS* 4.7 4.5 - - - -
103A GLU* 4.8 2.1 + - - -
115A GLN* 4.0 18.1 + - - +
116A LEU 3.5 3.4 - - - -
117A TRP* 3.6 24.0 - - + +
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Residues in contact with VAL 64 (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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62A GLU* 5.0 0.7 - - + -
63A THR* 1.3 78.1 - - - +
65A SER* 1.3 60.8 + - - +
90A LEU* 3.7 17.9 - - + -
91A GLN 3.4 3.6 - - - +
92A TRP* 3.5 59.9 - - + +
114A LEU 3.5 2.1 - - - +
115A GLN* 3.3 5.4 - - - -
116A LEU* 2.8 45.9 + - + +
118A VAL* 4.0 14.1 - - + -
171A TYR* 3.9 19.2 - - + -
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Residues in contact with SER 65 (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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63A THR* 4.0 3.0 + - - -
64A VAL* 1.3 71.8 + - - +
66A TYR* 1.3 59.9 + - - +
85A MET* 3.4 20.2 - - - +
90A LEU* 3.4 7.8 - - - +
91A GLN* 2.9 42.3 + - - -
103A GLU* 3.8 9.8 + - - -
114A LEU 3.5 6.1 - - - -
115A GLN* 2.9 25.3 + - - -
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Residues in contact with TYR 66 (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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64A VAL 5.4 0.2 - - - +
65A SER* 1.3 74.6 - - - +
67A LEU* 1.3 65.0 + - - +
68A LEU* 3.7 22.1 + - + -
85A MET* 4.8 0.4 - - - -
88A GLY* 3.6 28.4 + - - -
89A ASP 3.5 13.9 - - - -
90A LEU* 4.4 10.1 - - + -
113A GLY* 3.3 1.4 - - - -
114A LEU* 2.9 40.2 + - + +
139A ILE* 4.5 2.9 - - + +
141A LYS* 5.4 2.6 - - - -
150A ALA* 3.6 16.6 - - - +
152A ILE* 3.7 27.1 - - + -
171A TYR* 3.9 29.2 - + + +
173A ASP* 2.8 37.6 + - + -
239A VAL* 5.2 0.2 - - + -
1003A EDO 4.4 2.8 + - - -
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Residues in contact with LEU 67 (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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45A PHE* 6.1 0.9 - - + -
65A SER 4.4 0.2 - - - -
66A TYR* 1.3 77.9 - - - +
68A LEU* 1.3 71.4 + - - +
71A GLY 3.7 15.0 - - - +
73A MET* 3.7 26.2 - - + +
85A MET* 3.2 48.4 - - + +
86A ASN 3.7 17.3 - - - +
88A GLY* 2.8 27.0 + - - -
89A ASP 3.2 10.4 + - - +
111A ALA* 4.2 7.2 - - + -
112A HIS 3.6 17.5 - - - +
113A GLY* 4.0 9.4 - - - +
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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