Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 3EVK
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 GLN 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.7 22.4 - - + -
146A TYR* 3.7 7.8 - - - -
147A GLU* 2.9 31.2 + - + +
150A GLU* 4.2 4.6 - - - +
151A GLU* 1.3 78.4 - - - +
153A LEU* 1.3 67.4 + - - +
154A LEU* 4.0 19.6 - - + +
15D THR* 3.8 10.9 - - - +
16D LYS* 2.7 48.0 + - + +
18D TYR* 2.9 34.8 + - - +
58D LEU* 4.2 4.5 - - - +
65D ARG* 5.5 0.9 + - - -
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Residues in contact with LEU 153 (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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111A ILE* 4.5 5.8 - - + -
114A LEU* 3.8 36.3 - - + +
115A ILE* 3.9 17.7 - - + +
118A PHE* 3.7 25.2 - - + +
119A PHE* 3.9 24.0 - - + -
144A LEU* 4.1 10.3 - - + -
145A VAL 3.4 6.1 - - - +
146A TYR* 4.5 6.7 - - + -
152A GLN* 1.3 79.4 - - - +
154A LEU* 1.3 68.8 + - - +
172A LEU* 3.6 31.2 - - + -
210A LEU* 4.1 14.1 - - + -
65D ARG* 4.4 4.7 + - - -
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Residues in contact with LEU 154 (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 PHE* 4.7 2.7 - - - -
144A LEU* 3.5 5.4 - - - +
145A VAL* 2.8 46.2 + - + +
147A GLU* 3.9 18.8 - - + -
152A GLN* 3.7 16.6 + - + +
153A LEU* 1.3 82.2 - - - +
155A ILE* 1.3 67.1 + - - +
156A LEU* 5.0 3.4 - - + -
18D TYR* 4.3 4.9 - - - +
58D LEU* 3.8 28.5 - - + -
61D LEU* 5.5 0.4 - - + -
65D ARG* 4.5 10.3 - - - +
80D LEU* 4.2 18.8 - - + -
84D LEU* 3.6 30.7 - - + -
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Residues in contact with ILE 155 (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 PHE* 3.7 30.4 - - + -
125A PHE* 3.8 22.7 - - + -
128A GLU* 3.7 21.2 + - + +
129A PHE* 3.7 37.5 - - + +
132A ALA* 3.8 28.9 - - + -
142A ALA* 5.1 0.4 - - + -
143A ILE 3.3 9.6 - - - +
144A LEU* 4.2 2.5 - - + -
154A LEU* 1.3 77.0 - - - +
156A LEU* 1.3 72.0 + - - +
65D ARG* 5.1 1.8 - - - +
77D LEU* 3.3 25.6 - - + +
80D LEU* 4.4 3.3 - - - +
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Residues in contact with LEU 156 (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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142A ALA* 3.6 3.1 - - - -
143A ILE* 3.0 47.6 + - + +
145A VAL* 4.1 27.4 - - + -
154A LEU* 4.1 4.9 + - + -
155A ILE* 1.3 82.5 - - - +
157A GLN* 1.3 67.2 + - - +
158A ILE* 4.5 0.9 - - + -
164A MET 4.0 6.3 - - - +
166A ALA* 3.8 37.7 - - + +
77D LEU* 4.2 9.6 - - + +
80D LEU* 4.0 22.0 - - + -
81D SER* 4.6 22.2 - - - +
84D LEU* 5.5 1.6 - - + -
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Residues in contact with GLN 157 (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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132A ALA* 2.7 37.7 + - + +
135A ASN* 3.0 28.6 + - - +
136A VAL* 4.0 12.5 - - + +
141A TRP 3.5 5.4 - - - +
156A LEU* 1.3 73.3 - - - +
158A ILE* 1.3 65.7 + - - +
159A GLU* 5.0 3.1 - - + +
164A MET* 3.3 40.8 - - + +
74D ARG* 3.3 39.6 - - - +
77D LEU* 4.0 24.2 + - + +
78D ARG* 4.9 0.5 - - - +
81D SER* 5.6 0.5 - - - -
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Residues in contact with ILE 158 (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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136A VAL* 4.1 4.3 - - - +
140A GLY* 3.0 3.5 - - - -
141A TRP* 2.8 50.0 + - + +
143A ILE* 3.7 31.0 - - + -
156A LEU* 4.5 2.0 - - + -
157A GLN* 1.3 84.9 - - - +
159A GLU* 1.3 66.4 + - - +
160A LYS 4.0 5.2 - - - +
161A HIS* 3.6 35.0 - - - +
162A ASN 3.9 0.2 - - - +
163A LEU 3.3 7.6 - - - +
164A MET 3.6 3.8 - - - +
165A HIS* 3.5 48.5 - - + +
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Residues in contact with GLU 159 (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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136A VAL* 4.6 6.1 - - + -
137A GLU* 3.7 21.5 + - - +
139A VAL 3.5 4.9 - - - +
157A GLN* 5.0 2.4 - - + +
158A ILE* 1.3 73.4 - - - +
160A LYS* 1.3 73.3 + - + +
162A ASN 3.4 0.3 + - - -
163A LEU* 3.1 50.6 + - + +
164A MET* 3.6 19.1 - - + +
160C LYS* 2.7 31.8 + - - +
74D ARG* 5.0 1.4 - - - -
78D ARG* 2.8 33.1 + - - -
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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