Contacts of the strand formed by residues 172 - 178 (chain A) in PDB entry 5GGP
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 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.7 1.6 - - + -
134A ILE 3.6 0.7 - - - +
135A VAL* 3.3 8.0 - - - +
136A LEU* 2.9 57.3 + - + +
137A ASN 5.0 0.4 - - - +
138A GLN* 4.1 15.5 - - - +
171A ARG* 1.3 74.9 - - - +
173A LEU* 1.3 65.1 + - - +
174A ILE* 4.6 0.7 - - + -
213A VAL* 3.9 26.2 - - + -
214A GLY 3.7 7.9 - - - +
215A ARG* 4.1 20.0 - - - +
221A PHE* 4.7 4.3 - - + -
244A VAL* 4.0 25.6 - - + -
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Residues in contact with LEU 173 (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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133A VAL* 4.6 3.6 - - + -
134A ILE 3.5 2.7 - - - +
135A VAL* 4.0 25.8 - - + -
164A LEU* 4.1 21.1 - - + -
167A VAL* 4.1 15.5 - - + -
171A ARG 4.5 5.2 - - - +
172A VAL* 1.3 75.7 - - - +
174A ILE* 1.3 63.7 + - - +
175A CYS* 5.2 5.6 - - - -
196A LEU* 4.0 29.8 - - + -
212A PHE* 3.8 11.6 - - + +
213A VAL* 3.3 5.4 - - - +
214A GLY 2.6 40.5 + - - +
215A ARG 5.2 0.2 - - - -
216A LYS* 4.0 28.3 - - + +
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Residues in contact with ILE 174 (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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101A VAL* 4.0 12.8 - - + -
103A VAL* 3.6 31.2 - - + -
112A VAL* 4.0 31.2 - - + -
114A VAL* 4.8 1.3 - - + -
132A HIS 3.6 0.5 - - - +
133A VAL* 3.3 5.7 - - - +
134A ILE* 2.8 45.9 + - + +
136A LEU* 3.9 33.9 - - + -
172A VAL* 4.6 3.1 - - + -
173A LEU* 1.3 79.7 - - - +
175A CYS* 1.3 66.3 - - - +
176A THR* 5.1 0.7 - - + +
212A PHE 3.2 5.6 - - - +
213A VAL* 3.8 15.0 - - + -
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Residues in contact with CYS 175 (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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103A VAL* 3.9 2.1 - - - +
131A ILE* 4.3 2.9 - - + -
132A HIS 3.2 5.6 - - - +
133A VAL* 4.2 22.0 - - - -
160A MET* 6.1 0.2 - - - -
164A LEU* 5.7 4.9 - - - -
173A LEU* 5.2 5.2 - - - -
174A ILE* 1.3 81.7 - - - +
176A THR* 1.3 64.6 + - - +
193A LEU* 5.0 9.6 - - - -
196A LEU* 6.3 1.6 - - - -
210A TRP* 3.7 36.3 - - + -
211A ALA* 3.4 1.7 - - - -
212A PHE* 2.9 45.8 + - + +
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Residues in contact with THR 176 (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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103A VAL* 3.6 11.9 - - - +
104A TYR 2.8 24.0 + - - +
105A SER* 3.2 14.7 - - - -
110A VAL* 3.6 20.1 - - + +
112A VAL* 4.2 20.4 - - + -
120A LEU* 4.4 0.7 - - + -
130A GLY 3.6 0.5 - - - +
131A ILE* 4.5 2.4 - - - +
132A HIS* 2.8 52.9 + - + +
134A ILE* 6.1 0.2 - - + -
174A ILE* 5.4 0.7 - - + -
175A CYS* 1.3 78.7 - - - +
177A VAL* 1.3 62.8 + - - +
210A TRP* 3.3 5.8 + - - -
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Residues in contact with VAL 177 (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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105A SER* 2.7 26.8 + - - +
106A SER 3.4 7.3 + - - +
110A VAL* 3.3 10.1 - - - +
130A GLY 3.3 4.9 - - - +
131A ILE* 4.1 16.6 - - + -
176A THR* 1.3 75.0 + - - +
178A LYS* 1.3 72.6 + - - +
179A ASP 4.2 1.3 - - - +
180A GLU 4.0 2.7 - - - +
181A GLY* 3.8 21.1 - - - +
204A LEU* 4.1 12.3 - - + -
208A ASP 3.8 15.9 - - - +
209A THR* 5.9 0.4 - - + -
210A TRP* 3.1 44.4 + - + +
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Residues in contact with LYS 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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106A SER 3.5 5.4 - - - +
107A ARG 4.0 9.2 - - - +
108A SER* 3.9 13.9 - - - +
109A LYS* 4.2 5.2 - - - +
110A VAL* 3.6 16.9 - - + +
122A ASP* 2.5 47.7 + - - +
124A ALA 2.7 24.5 + - - +
127A GLN 2.7 24.0 + - - -
128A GLY 3.5 20.9 - - - +
129A ARG* 3.6 1.5 - - - +
130A GLY 2.9 26.7 + - - +
132A HIS* 4.0 3.6 - - - +
176A THR 3.8 0.6 + - - -
177A VAL* 1.3 74.1 - - - +
179A ASP* 1.3 65.4 + - + +
180A GLU 2.8 16.8 + - - -
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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