Contacts of the strand formed by residues 117 - 125 (chain A) in PDB entry 6QPA
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 PRO 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA* 3.5 2.4 - - - -
10A ILE 3.0 41.3 + - - +
12A MET* 4.0 14.1 - - + -
115A TRP* 3.3 30.7 - - + +
116A GLU* 1.3 87.9 - - - +
118A TYR* 1.3 60.8 + - - +
119A PHE* 3.6 22.1 - - + -
201A GLN* 3.8 23.1 - - + +
203A GLY 3.3 13.0 - - - +
204A VAL* 3.9 6.1 - - + -
252A GLN* 5.0 0.4 - - - +
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Residues in contact with TYR 118 (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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7A ILE* 3.7 20.6 - - + -
8A ILE 3.6 1.3 - - - -
9A ALA* 4.1 12.8 - - + -
82A TRP* 5.4 0.4 - + - -
85A VAL* 3.9 23.3 + - + -
88A HIS* 2.6 40.6 + + + +
89A GLU* 2.5 37.2 + - - +
117A PRO* 1.3 74.6 - - - +
119A PHE* 1.3 61.0 - - - +
201A GLN* 3.4 6.6 - - - +
202A PHE* 3.1 43.0 + - + -
203A GLY 2.6 14.3 + - - +
204A VAL 3.9 1.6 - - - -
205A SER* 3.5 24.5 - - - -
243A PRO* 3.6 26.0 - - + -
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Residues in contact with PHE 119 (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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7A ILE* 3.7 6.9 - - - -
8A ILE* 2.7 40.3 + - + +
10A ILE* 3.6 31.6 - - + -
12A MET* 4.0 3.4 - - + -
117A PRO* 3.6 35.7 - - + -
118A TYR* 1.3 75.5 - - - +
120A GLU* 1.3 60.3 + - - +
121A VAL 4.0 0.5 + - - -
199A MET* 3.8 32.5 - - + -
200A LYS 3.3 5.6 - - - +
201A GLN* 3.5 31.2 - - + -
202A PHE* 3.5 6.7 - - - -
252A GLN* 3.6 14.4 - - - -
254A LEU* 3.5 34.1 - - + -
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Residues in contact with GLU 120 (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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5A ASN* 6.5 1.1 - - + -
6A PRO 5.0 0.2 - - - -
7A ILE* 4.8 9.0 - - + -
119A PHE* 1.3 74.7 - - - +
121A VAL* 1.3 69.8 + - - +
122A VAL* 3.3 21.8 + - + +
199A MET* 3.2 6.5 - - - -
200A LYS* 2.9 51.5 + - + +
202A PHE* 3.6 18.8 - - + +
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Residues in contact with VAL 121 (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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5A ASN* 5.2 11.7 - - - +
6A PRO* 3.9 22.0 + - + +
8A ILE* 3.8 31.6 - - + -
119A PHE 4.0 0.4 + - - +
120A GLU* 1.3 78.4 - - - +
122A VAL* 1.3 63.6 + - - +
123A LYS* 4.1 6.1 - - - +
124A SER* 4.0 19.7 - - - +
197A MET* 3.8 27.1 - - + -
198A ILE 3.6 3.1 - - - -
199A MET* 4.8 2.7 - - + +
312A LEU* 4.5 16.6 - - + -
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Residues in contact with VAL 122 (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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120A GLU* 4.0 18.6 - - - +
121A VAL* 1.3 73.2 - - - +
123A LYS* 1.3 68.7 + - + +
176A GLU* 3.5 44.0 - - + +
180A THR* 5.7 0.7 - - - +
198A ILE* 2.8 25.2 + - + +
200A LYS* 3.7 30.3 - - + -
253A TYR* 4.1 5.4 - - + -
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Residues in contact with LYS 123 (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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121A VAL* 3.4 5.0 - - - +
122A VAL* 1.3 85.6 - - + +
124A SER* 1.3 71.7 + - - +
180A THR* 4.2 24.7 - - + +
184A GLU* 3.7 21.0 + - - -
196A TRP* 3.4 21.5 - - + -
198A ILE* 2.9 29.4 + - + +
313A LYS* 6.3 0.8 - - - +
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Residues in contact with SER 124 (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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121A VAL* 4.0 16.1 - - - +
123A LYS* 1.3 87.1 + - - +
125A ASP* 1.3 63.2 + - - +
126A LEU* 4.4 2.3 + - - -
196A TRP* 3.4 20.9 - - - -
197A MET* 4.1 8.1 - - - -
312A LEU* 3.8 32.3 - - - +
313A LYS* 4.2 23.7 + - - +
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Residues in contact with ASP 125 (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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124A SER* 1.3 73.4 - - - +
126A LEU* 1.3 59.6 + - - +
127A PRO 5.1 0.3 - - - -
187A LYS* 3.0 37.0 + - - +
195A GLY* 3.2 9.4 - - - -
196A TRP* 2.9 52.2 + - + +
313A LYS* 5.6 5.0 - - - +
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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