Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 3FL7
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 GLY 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A TRP* 3.6 15.0 - - - -
86A VAL 3.0 15.3 - - - -
88A ARG* 3.9 6.7 - - - -
125A GLU* 3.7 2.8 - - - +
126A SER 2.8 29.8 + - - +
175A ARG* 3.3 5.9 - - - +
176A LYS* 1.3 77.7 - - - +
178A PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 178 (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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31A LEU* 4.2 7.9 - - + -
85A TRP* 3.7 4.9 - - - +
86A VAL* 2.8 72.5 + - + +
88A ARG* 4.4 10.5 - - + -
94A ILE* 3.7 42.2 - - + -
123A TYR* 5.0 4.5 - + + -
124A ALA 3.1 16.4 - - - +
125A GLU* 4.2 9.9 - - + +
126A SER 4.7 0.7 - - - +
173A LEU* 4.2 19.3 - - + -
177A GLY* 1.3 77.9 - - - +
179A TYR* 1.3 76.5 + - - +
180A LEU* 4.4 13.5 - - + -
196A VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 179 (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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82A ARG* 3.5 31.5 + - - -
83A THR* 3.3 22.2 - - - -
85A TRP* 3.5 39.0 - + + -
123A TYR* 3.1 9.2 - - - +
124A ALA* 2.8 37.8 + - + +
126A SER* 4.4 5.8 - - - -
129A ASP* 3.2 11.7 + - - -
130A TYR* 2.8 54.7 + + - +
139A PHE* 3.6 29.4 - + + -
178A PHE* 1.3 78.8 - - - +
180A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 180 (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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32A LEU* 4.8 2.2 - - + -
82A ARG* 3.5 6.4 - - - +
83A THR* 3.0 44.6 + - + +
94A ILE* 4.6 1.1 - - + -
96A ILE* 3.7 42.4 - - + -
121A LEU* 4.6 2.7 - - + -
122A TYR 3.5 12.6 - - - +
123A TYR* 4.0 9.4 - - + -
139A PHE* 4.2 1.1 - - - -
142A ILE* 4.5 1.3 - - + -
178A PHE* 4.4 17.6 - - + -
179A TYR* 1.3 80.2 - - - +
181A ALA* 1.3 63.5 + - - +
182A PHE* 4.4 9.0 - - + -
194A VAL* 4.1 14.4 - - + -
196A VAL* 3.6 26.5 - - + -
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Residues in contact with ALA 181 (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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80A TRP* 4.0 21.8 - - + -
81A LEU 3.0 14.6 - - - +
82A ARG* 4.3 6.1 - - + -
121A LEU* 3.6 4.3 - - - +
122A TYR* 3.2 25.9 + - + +
134A PHE* 4.8 1.1 - - + -
139A PHE* 3.9 24.7 - - + -
180A LEU* 1.3 76.5 - - - +
182A PHE* 1.3 78.2 + - - +
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Residues in contact with PHE 182 (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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43A TRP* 4.6 6.7 - + - -
52A TRP* 3.7 22.7 + - + -
79A ASN 3.3 4.9 - - - +
80A TRP* 3.4 5.8 - - - +
81A LEU* 3.0 46.9 + - + +
83A THR* 4.1 17.9 - - + -
98A LEU* 3.7 26.7 - - + -
119A PHE* 3.8 17.3 - + + -
120A ASN 3.2 8.7 - - - +
121A LEU* 3.8 19.3 - - + -
122A TYR* 5.1 0.4 - - - +
180A LEU* 4.4 3.8 - - + -
181A ALA* 1.3 101.2 - - - +
183A GLN* 1.3 62.2 + - - +
191A LEU* 3.8 20.2 - - + -
194A VAL* 4.1 24.9 - - + -
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Residues in contact with GLN 183 (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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52A TRP* 4.3 0.9 - - - -
78A ASP* 2.7 26.1 + - - +
79A ASN 3.3 4.5 - - - +
80A TRP* 3.5 24.2 - - + +
119A PHE* 3.2 9.5 - - - +
120A ASN* 2.8 49.7 + - + +
122A TYR* 2.8 36.0 + - + -
136A LYS* 5.1 1.2 - - - +
182A PHE* 1.3 76.0 - - - +
184A ASP* 1.3 63.7 - - - +
185A ILE* 3.2 26.5 + - + +
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Residues in contact with ASP 184 (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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52A TRP* 3.7 26.2 - - + +
69A VAL* 3.3 19.8 - - + +
77A GLN* 3.1 10.2 + - - -
78A ASP* 3.7 1.0 - - - -
79A ASN* 2.9 58.5 + - + +
118A THR 5.4 0.2 - - - -
119A PHE* 4.6 6.1 - - + +
183A GLN* 1.3 74.3 - - - +
185A ILE* 1.3 64.7 + - - +
186A GLY 2.9 3.0 + - - -
187A ALA* 2.6 40.9 + - + +
189A VAL* 5.4 0.4 - - + -
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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