Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 6FF7
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ASN* 6.2 3.8 - - + -
114A ARG* 3.9 9.4 - - + +
115A ASP* 1.3 75.6 - - - +
117A PRO* 1.3 68.6 - - - +
118A VAL* 5.0 0.2 - - - +
129A VAL* 5.9 4.0 - - + -
131A GLU* 5.9 4.7 - - + -
486A LYS* 4.4 4.6 - - - +
487A LEU* 2.9 35.7 + - - +
488A ASP 5.5 0.4 - - - -
489A TRP* 5.3 7.6 - - + -
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Residues in contact with PRO 117 (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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116A VAL* 1.3 79.8 - - - +
118A VAL* 1.3 64.4 + - - +
129A VAL* 3.9 9.0 - - - +
130A ASN* 3.8 29.7 + - + +
131A GLU* 5.5 6.9 - - + +
484A SER* 6.5 0.4 - - - -
485A THR 3.5 9.9 - - - +
486A LYS* 4.0 8.0 - - + -
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Residues in contact with VAL 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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116A VAL 5.0 1.3 - - - +
117A PRO* 1.3 78.6 - - - +
119A LEU* 1.3 62.6 + - - +
120A TYR* 4.2 3.8 - - + +
127A SER* 5.3 9.6 - - - +
128A PHE 3.2 11.4 - - - +
129A VAL* 4.1 5.4 - - + +
130A ASN* 4.3 5.2 - - - +
483A GLN 4.5 0.2 - - - -
484A SER* 3.4 23.9 - - - -
485A THR* 2.9 16.7 + - - +
487A LEU* 5.1 11.4 - - + -
492A VAL* 5.7 8.7 - - + -
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Residues in contact with LEU 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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118A VAL* 1.3 71.3 - - - +
120A TYR* 1.3 57.8 + - - +
126A ILE 4.0 1.4 - - - +
128A PHE* 2.4 60.8 + - + +
130A ASN* 4.5 12.3 - - + -
473A PHE* 6.1 3.4 - - + +
476A PHE* 6.2 2.9 - - + -
477A LYS* 6.3 2.9 - - + -
482A PHE* 5.5 6.3 - - + -
483A GLN 3.3 12.3 - - - +
484A SER* 5.1 3.6 - - - -
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Residues in contact with TYR 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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66A VAL* 5.4 11.9 - - + -
118A VAL* 4.2 4.2 - - + -
119A LEU* 1.3 75.2 - - - +
121A HIS* 1.3 66.3 + - - +
124A GLY* 6.3 0.4 - - - -
126A ILE 3.4 6.5 - - - +
127A SER* 3.9 20.9 - - - +
482A PHE* 3.2 7.7 - - - -
483A GLN* 2.9 35.6 + - + +
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Residues in contact with HIS 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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69A ILE* 6.0 0.2 - - - +
120A TYR* 1.3 80.7 - - - +
122A ILE* 1.3 66.7 + - - +
123A THR 3.4 2.0 - - - +
124A GLY* 3.2 12.6 + - - +
125A ALA* 3.6 34.1 - - + +
126A ILE* 3.1 12.0 + - + +
481A PHE* 3.3 10.3 - - + +
482A PHE* 4.7 0.9 - - - +
483A GLN* 6.3 0.2 - - - -
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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