Contacts of the strand formed by residues 162 - 170 (chain A) in PDB entry 3EFC
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 ARG 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 4.0 8.1 - - - +
92A PRO* 5.0 0.2 - - - +
93A THR* 3.2 16.8 - - + +
95A ALA* 3.8 15.6 - - + +
157A PRO* 4.0 1.2 - - - +
158A LEU* 2.9 42.9 + - + +
159A PRO* 2.9 39.2 - - - +
160A ARG* 2.9 57.1 - - + +
161A ASN* 1.3 80.4 - - - +
163A VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 3.0 40.2 - - + -
93A THR 3.0 10.5 + - - +
94A ILE* 3.8 5.0 - - + +
95A ALA* 2.9 25.6 + - - +
96A SER 3.8 0.9 + - - +
125A LEU* 4.8 13.7 - - + -
127A ARG* 4.3 12.3 - - - +
155A VAL* 4.1 12.6 - - + -
156A THR 3.7 29.8 - - - +
157A PRO* 3.9 7.6 - - + -
158A LEU* 4.0 4.9 - - - +
162A ARG* 1.3 72.5 - - - +
164A ASP* 1.3 64.7 + - - +
165A LEU* 4.3 0.6 + - - +
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Residues in contact with ASP 164 (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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96A SER* 2.7 26.8 + - - +
98A THR* 2.9 22.0 + - - -
154A VAL 3.8 0.2 - - - +
155A VAL* 3.2 9.5 - - - -
156A THR* 3.1 47.3 + - + +
158A LEU* 3.8 15.9 - - + +
163A VAL* 1.3 75.8 - - - +
165A LEU* 1.3 82.4 + - - +
166A LYS* 3.9 1.8 + - - +
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Residues in contact with LEU 165 (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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94A ILE* 4.1 26.5 - - + -
96A SER 2.8 13.2 + - - +
97A ILE* 3.5 23.1 - - + +
98A THR 2.7 29.6 + - - +
114A LEU* 5.1 0.4 - - + -
119A VAL* 4.3 9.4 - - + -
125A LEU* 5.4 4.9 - - + -
133A ILE* 5.3 11.7 - - + -
153A ALA* 5.3 2.0 - - + -
154A VAL 4.0 10.1 - - - +
155A VAL* 5.6 2.2 - - + -
163A VAL 5.5 0.2 - - - +
164A ASP* 1.3 85.9 + - - +
166A LYS* 1.3 60.2 + - - +
167A LEU* 3.5 35.3 + - + -
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Residues in contact with LYS 166 (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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98A THR* 3.3 18.6 - - + +
100A SER* 5.9 3.1 - - - -
152A LYS 3.9 0.5 - - - +
154A VAL* 2.9 53.9 + - + +
156A THR* 5.4 2.9 + - - +
164A ASP* 3.9 3.1 + - - +
165A LEU* 1.3 73.6 - - - +
167A LEU* 1.3 61.9 + - - +
168A VAL* 3.9 7.9 - - + -
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Residues in contact with LEU 167 (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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97A ILE* 4.6 0.7 - - + -
98A THR 2.9 6.9 + - - +
99A PHE* 3.8 12.1 - - + -
100A SER 3.2 22.5 + - - -
114A LEU* 3.4 30.5 - - + -
133A ILE* 4.6 8.1 - - + -
134A GLU* 5.6 0.2 - - + -
137A LEU* 3.3 31.9 - - + -
151A VAL* 4.3 5.6 - - + -
152A LYS 3.6 1.6 - - - +
153A ALA* 3.7 26.2 - - + -
165A LEU* 3.5 28.7 - - + +
166A LYS* 1.3 71.0 - - - +
168A VAL* 1.3 61.0 + - - +
169A PHE* 3.3 22.2 - - + -
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Residues in contact with VAL 168 (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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100A SER* 3.3 26.7 - - - +
101A GLY* 5.9 0.2 - - - -
150A SER 3.8 0.2 - - - +
151A VAL* 3.5 3.0 - - - +
152A LYS* 2.9 53.6 + - + +
154A VAL* 5.5 5.6 - - + -
166A LYS* 3.9 10.7 - - + +
167A LEU* 1.3 74.5 - - - +
169A PHE* 1.3 68.7 + - - +
170A GLN* 3.7 13.0 + - + +
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Residues in contact with PHE 169 (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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99A PHE* 3.9 15.3 - + + -
100A SER 3.1 10.2 + - - -
101A GLY* 3.1 29.5 - - - +
102A ASN* 3.9 19.3 - - + +
110A LEU* 3.3 30.3 - - + -
137A LEU* 4.2 17.5 - - + -
141A TYR* 4.2 22.0 - + + +
150A SER 3.9 3.4 - - - +
151A VAL* 3.5 33.7 - - + -
167A LEU* 3.3 35.9 - - + -
168A VAL* 1.3 74.8 - - - +
170A GLN* 1.3 60.2 + - - +
171A GLU* 3.0 11.2 + - - +
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Residues in contact with GLN 170 (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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150A SER* 3.3 39.8 + - - +
168A VAL* 3.7 12.2 + - + +
169A PHE* 1.3 68.5 - - - +
171A GLU* 1.3 71.4 + - - +
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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