Contacts of the strand formed by residues 126 - 130 (chain A) in PDB entry 2A7P
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA* 4.3 8.3 - - + -
99A THR* 5.2 0.9 - - - +
105A PHE* 3.6 20.6 - - + -
118A LEU* 3.7 34.8 - - + +
119A ALA* 3.8 23.6 - - + -
122A CYS* 4.0 18.4 - - + +
124A GLY* 3.2 13.2 + - - +
125A ASP* 1.3 79.5 + - - +
127A TRP* 1.3 64.0 + - - +
149A GLY 5.6 1.1 + - - +
150A TYR* 3.3 34.8 - - + +
151A THR* 3.1 27.8 + - - +
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Residues in contact with TRP 127 (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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66A VAL* 4.2 18.8 - - + -
67A LEU* 4.1 20.4 - - + -
69A LYS* 5.4 2.9 - - - +
71A GLN* 5.3 0.2 - - - -
76A LEU* 3.5 31.2 - - + -
104A PRO* 3.7 17.1 - - + +
105A PHE 2.8 12.8 + - - +
106A VAL* 3.8 15.9 - - + -
107A LEU 2.8 25.0 + - - -
125A ASP* 3.2 36.0 + - - -
126A LEU* 1.3 73.7 - - - +
128A PHE* 1.3 61.9 + - - +
150A TYR* 3.6 7.6 - - - -
151A THR* 3.4 6.5 - - - -
152A THR* 3.3 38.1 + - + +
154A VAL* 4.0 13.5 - - + -
229A LEU* 3.8 22.2 - - + -
251A ILE* 5.4 3.1 - - + -
282A LEU* 4.5 4.5 - - + -
305A LEU* 5.7 0.2 - - + -
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Residues in contact with PHE 128 (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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106A VAL* 4.2 2.0 - - - -
107A LEU* 3.3 22.0 - - + -
108A SER 4.1 4.0 - - - -
109A THR* 3.5 22.9 - - - -
115A ILE* 3.5 37.2 - - + -
127A TRP* 1.3 74.1 - - - +
129A GLN* 1.3 71.3 - - - +
130A LEU* 4.1 13.7 - - + -
141A MET* 4.0 24.0 - - + -
142A VAL* 4.7 0.7 - - - -
145A ALA* 3.9 22.4 - - + -
150A TYR* 3.8 15.2 - + + -
152A THR 2.8 12.4 + - - +
153A LEU* 3.4 22.7 - - + +
154A VAL* 2.8 30.3 + - - -
183A ASN* 4.4 1.3 - - - -
224A TRP* 6.1 0.4 - - + -
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Residues in contact with GLN 129 (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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79A PRO* 3.4 23.6 - - + -
106A VAL* 3.6 7.1 - - + +
107A LEU 2.9 7.9 + - - +
108A SER* 3.2 7.1 + - - +
109A THR* 2.8 41.4 + - - +
128A PHE* 1.3 85.1 - - - +
130A LEU* 1.3 81.6 + - - +
131A TYR* 3.4 16.9 - - - -
154A VAL* 3.2 13.7 - - + +
156A THR* 3.1 24.7 + - - +
390A FMN 2.9 33.4 + - - +
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Residues in contact with LEU 130 (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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109A THR* 3.1 8.1 - - - +
128A PHE* 4.1 14.1 - - + -
129A GLN* 1.3 81.4 - - - +
131A TYR* 1.3 77.3 + - - +
132A VAL* 4.1 16.2 - - + -
138A ALA* 4.2 23.8 - - + +
141A MET* 4.3 9.6 - - + -
142A VAL* 3.9 19.3 - - + -
153A LEU* 4.0 14.1 - - + -
154A VAL 2.6 14.7 + - - +
155A LEU* 3.7 10.3 - - + +
156A THR 3.3 23.4 + - - +
219A TRP* 6.0 0.7 - - + -
220A LEU* 4.2 24.7 - - + -
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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