Contacts of the strand formed by residues 99 - 105 (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 LEU 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A VAL* 1.3 74.2 - - - +
100A ASP* 1.3 60.5 + - - +
101A VAL* 3.4 12.5 + - + +
114A VAL* 4.1 9.4 - - + -
115A ASP* 3.3 23.3 - - - +
136A LEU* 4.1 18.8 - - + -
137A ASN 5.1 1.1 - - - +
140A THR 4.1 5.6 - - - +
141A GLY* 3.5 34.1 - - - -
172A VAL* 5.7 2.2 - - + -
243A ASP* 3.3 8.8 - - - -
244A VAL* 2.6 49.6 + - + +
246A LEU* 3.6 29.8 - - + -
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Residues in contact with ASP 100 (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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98A VAL* 4.1 1.4 + - - +
99A LEU* 1.3 69.9 - - - +
101A VAL* 1.3 64.2 + - - +
102A GLU* 4.4 2.4 - - - +
113A ALA 3.7 0.9 - - - +
114A VAL* 3.3 4.0 - - - -
115A ASP* 2.7 51.7 + - - +
116A GLY 4.6 2.1 + - - -
241A LYS* 2.9 41.7 + - - +
242A THR 4.0 3.5 - - - +
243A ASP* 4.1 10.8 - - - +
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Residues in contact with VAL 101 (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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99A LEU* 3.9 15.5 - - + +
100A ASP* 1.3 78.5 + - - +
102A GLU* 1.3 64.6 + - - +
103A VAL* 3.8 23.1 - - + -
112A VAL* 4.8 0.4 - - + -
113A ALA 3.4 7.4 - - - +
114A VAL* 4.5 11.0 - - + -
136A LEU* 4.8 7.4 - - + -
174A ILE* 4.0 18.2 - - + -
213A VAL* 4.1 9.0 - - + -
240A LEU 3.6 1.2 - - - +
241A LYS* 3.3 3.8 - - - +
242A THR* 2.9 42.0 + - + +
244A VAL* 3.6 27.8 - - + -
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Residues in contact with GLU 102 (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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100A ASP* 4.4 2.0 - - - +
101A VAL* 1.3 75.3 - - - +
103A VAL* 1.3 66.2 + - - +
104A TYR 4.3 0.2 - - - -
111A TYR* 2.3 44.8 + - + +
112A VAL* 3.2 7.4 - - - +
113A ALA* 2.9 41.2 + - + +
239A LEU* 4.9 6.1 - - + -
240A LEU 3.2 4.0 - - - +
241A LYS* 3.0 46.8 + - + +
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Residues in contact with VAL 103 (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* 3.8 9.4 - - + -
102A GLU* 1.3 80.5 - - - +
104A TYR* 1.3 62.5 + - - +
111A TYR 3.7 2.0 - - - -
112A VAL* 4.1 5.8 - - + -
174A ILE* 3.6 16.8 - - + -
175A CYS 3.9 7.2 - - - +
176A THR* 3.6 28.0 - - - -
211A ALA* 3.8 18.2 - - + +
212A PHE 4.5 0.9 - - - +
213A VAL* 3.6 30.1 - - + -
238A VAL 3.7 1.4 - - - +
239A LEU* 3.7 2.9 - - - +
240A LEU* 2.7 46.4 + - + +
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Residues in contact with TYR 104 (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* 1.3 73.7 - - - +
105A SER* 1.3 54.3 - - - +
106A SER* 3.5 21.3 + - - -
109A LYS* 3.6 34.2 - - + -
110A VAL* 3.4 18.7 - - - -
111A TYR* 2.9 45.4 + + + +
176A THR* 2.8 18.1 + - - -
237A PRO* 3.5 34.9 - - + +
238A VAL 3.4 14.1 - - - -
239A LEU* 3.9 21.8 - - + -
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Residues in contact with SER 105 (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 4.3 0.4 + - - -
104A TYR* 1.3 72.9 - - - +
106A SER* 1.3 64.9 + - - +
109A LYS 4.0 0.2 - - - -
110A VAL* 4.2 0.2 - - - -
176A THR* 3.2 9.9 - - - -
177A VAL 2.7 20.0 + - - -
209A THR* 3.4 7.4 - - - +
210A TRP 2.9 47.8 + - - -
211A ALA* 4.4 0.4 - - - -
237A PRO* 3.2 2.8 - - - +
238A VAL* 3.0 37.5 + - - +
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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