Contacts of the strand formed by residues 138 - 143 (chain A) in PDB entry 6FF8
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 ALA 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ALA 3.3 8.1 - - - +
104A VAL* 4.6 4.0 - - + -
121A LYS* 3.7 31.0 - - + -
124A LEU* 4.5 13.5 - - + -
136A ILE 3.4 5.1 + - - +
137A PRO* 1.3 76.6 - - - +
139A VAL* 1.3 61.0 + - - +
166A GLY 4.6 3.2 + - - +
167A PHE* 3.3 13.9 - - + -
168A ALA 2.8 34.4 + - - +
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Residues in contact with VAL 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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102A ALA 3.0 6.4 + - - +
103A PHE* 3.5 20.5 - - + -
104A VAL 3.0 24.1 + - - -
138A ALA* 1.3 77.3 - - - +
140A LEU* 1.3 64.5 + - - +
141A LEU* 3.7 11.2 + - + -
167A PHE* 4.2 2.7 - - - -
168A ALA* 4.4 4.3 - - + -
169A GLY 3.7 8.7 - - - +
171A PHE* 3.7 33.4 - - + -
184A ALA 4.7 1.6 - - - +
187A PHE* 3.8 28.0 - - + -
188A LEU* 4.0 22.9 - - + -
191A LYS* 5.7 0.2 - - + -
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Residues in contact with LEU 140 (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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104A VAL 3.4 13.5 - - - +
106A PHE* 4.0 19.3 - - + -
114A PHE* 4.4 1.6 - - + -
117A VAL* 4.0 28.5 - - + -
139A VAL* 1.3 72.3 - - - +
141A LEU* 1.3 62.2 + - - +
142A ALA 4.0 0.4 - - - -
161A PHE* 3.9 18.4 - - + -
162A CYS* 4.9 0.2 - - - -
167A PHE* 4.0 30.9 - - + -
169A GLY 3.0 15.2 + - - +
170A TRP* 3.3 41.7 - - + -
171A PHE 3.0 25.6 + - - -
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Residues in contact with LEU 141 (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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41A ILE* 4.2 22.9 - - + -
103A PHE* 3.6 43.5 - - + -
104A VAL 2.9 8.7 + - - -
105A VAL* 3.4 20.7 - - + +
106A PHE* 3.0 28.3 + - - +
139A VAL* 4.2 4.3 - - + +
140A LEU* 1.3 77.3 - - - +
142A ALA* 1.3 61.3 + - - +
143A ASN 3.2 3.3 + - - -
171A PHE* 3.4 7.0 - - + -
173A THR* 4.0 22.4 - - + +
181A ILE* 5.9 0.9 - - + -
184A ALA* 3.6 29.6 - - + -
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Residues in contact with ALA 142 (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 PHE* 3.4 34.2 - - + -
108A ILE* 3.8 24.7 - - + +
140A LEU 4.0 0.8 - - - -
141A LEU* 1.3 69.7 - - - +
143A ASN* 1.3 63.2 + - - +
145A CYS* 4.3 0.7 - - - +
170A TRP* 4.0 15.5 - - + +
171A PHE 2.8 14.0 + - - +
172A GLU* 3.3 6.5 - - - +
173A THR 2.9 21.6 + - - +
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Residues in contact with ASN 143 (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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36A VAL 3.2 19.6 + - - +
37A GLY* 3.6 7.5 - - - -
41A ILE* 3.4 21.8 - - + +
105A VAL* 3.9 4.0 - - + -
106A PHE 2.7 17.3 + - - +
107A ASP* 3.6 0.7 - - - -
108A ILE* 2.9 25.6 + - - +
141A LEU 3.2 0.6 + - - +
142A ALA* 1.3 73.1 - - - +
144A LYS* 1.3 75.7 + - - +
173A THR* 2.8 31.1 + - - +
175A ALA 3.4 15.6 + - - -
900A GTP 3.1 29.7 + - - -
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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