Contacts of the strand formed by residues 134 - 139 (chain A) in PDB entry 6ACQ
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.2 16.2 - - + -
112A LEU* 3.2 28.5 - - + +
121A ILE* 4.0 16.1 - - + +
124A VAL* 4.6 2.0 - - + -
125A ALA* 3.5 34.6 - - + +
128A THR* 3.9 15.7 - - - +
130A ARG 3.6 12.6 - - - +
131A PRO 3.5 4.6 + - - +
132A ASP 3.5 1.4 + - - -
133A LYS* 1.3 82.9 - - - +
135A ILE* 1.3 60.3 + - - +
157A THR* 2.7 30.0 + - - +
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Residues in contact with ILE 135 (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* 4.0 10.1 - - + -
112A LEU 3.0 7.3 + - - +
113A ALA* 3.0 23.4 - - + -
114A SER 3.0 21.7 + - - -
121A ILE* 3.7 10.4 - - - +
134A VAL* 1.3 77.4 - - - +
136A GLY* 1.3 68.7 + - - +
151A VAL* 3.6 24.5 - - + -
152A ILE 3.2 14.8 - - - +
153A ARG* 4.7 1.3 - - + -
157A THR* 3.8 23.6 - - + -
161A THR* 4.2 4.9 - - + -
162A PHE* 3.9 20.6 - - + -
165A VAL* 4.0 25.8 - - + -
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Residues in contact with GLY 136 (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 SER 3.4 8.1 - - - -
121A ILE* 3.7 18.9 - - - +
135A ILE* 1.3 80.4 - - - +
137A MET* 1.3 60.2 + - - +
138A HIS 4.0 0.9 - - - -
151A VAL* 3.5 6.8 - - - +
152A ILE* 2.7 48.5 + - - -
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Residues in contact with MET 137 (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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20A PHE* 4.3 17.9 - - + -
83A LEU* 4.1 13.2 - - + -
85A ILE* 4.1 20.6 - - + +
113A ALA* 4.1 15.0 - - + -
114A SER 2.7 11.9 + - - +
115A ASN* 3.2 23.0 - - - +
135A ILE 3.9 1.0 + - - -
136A GLY* 1.3 71.0 - - - +
138A HIS* 1.3 61.8 + - - +
139A PHE* 3.6 31.3 - - + -
149A VAL* 4.1 12.3 - - + -
150A GLU 3.8 1.3 - - - -
151A VAL* 4.9 0.4 - - + -
165A VAL* 3.7 31.0 - - + +
168A THR* 4.8 2.7 - - - +
169A SER* 3.7 25.4 - - - +
172A ILE* 5.1 0.9 - - + -
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Residues in contact with HIS 138 (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 SER 5.5 0.2 - - - +
115A ASN* 3.3 23.6 - - - -
116A THR 3.7 7.4 - - - +
117A SER* 3.6 22.6 + - - -
137A MET* 1.3 70.9 - - - +
139A PHE* 1.3 70.5 + - - +
140A PHE* 3.7 22.8 - + - -
149A VAL* 3.2 7.7 - - - +
150A GLU* 2.8 74.3 + - + +
152A ILE* 4.5 2.5 - - + -
185A PHE* 3.6 22.8 - + + -
188A ASN* 4.2 12.3 + - - -
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Residues in contact with PHE 139 (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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12A MET* 3.3 28.3 - - + +
16A ILE* 3.6 48.5 - - + -
19A ALA* 5.2 1.6 - - + -
20A PHE* 4.3 7.2 - + - -
85A ILE* 4.5 4.7 - - + -
115A ASN* 3.0 8.0 + - + +
137A MET* 3.6 49.6 - - + -
138A HIS* 1.3 88.6 + - - +
140A PHE* 1.3 69.0 + - - +
143A ALA* 4.4 9.6 - - + -
146A MET 5.7 0.9 - - - -
148A LEU 4.3 2.5 - - - -
149A VAL* 3.8 21.8 - - + -
172A ILE* 4.3 7.2 - - + -
174A LYS* 4.0 22.2 - - - -
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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