Contacts of the strand formed by residues 209 - 215 (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 THR 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER* 3.4 14.4 - - - +
106A SER* 3.7 30.5 - - - -
107A ARG 4.4 0.4 - - - +
177A VAL* 4.8 1.8 - - + +
207A ARG 3.9 1.1 + - - +
208A ASP* 1.3 76.7 - - - +
210A TRP* 1.3 62.3 + - - +
225A HIS* 3.1 24.3 - - - -
226A SER* 3.0 26.2 + - - -
234A TRP* 5.5 1.6 - - + -
235A GLY* 3.6 22.0 - - - +
236A ASP 2.7 23.1 + - - +
238A VAL* 3.8 4.8 - - - +
302A NA 3.8 1.8 - - - -
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Residues in contact with TRP 210 (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* 2.9 14.1 + - - -
131A ILE* 4.1 16.8 - - + -
175A CYS* 3.7 31.9 - - + -
176A THR* 3.3 4.0 - - - -
177A VAL* 3.1 43.5 + - + +
193A LEU* 3.7 32.3 - - + -
198A SER* 3.3 20.6 - - - -
200A ALA* 3.8 13.9 - - + -
201A GLY* 3.8 8.7 - - - +
204A LEU* 3.7 24.5 - - + -
209A THR* 1.3 76.9 - - - +
211A ALA* 1.3 69.0 + - - +
212A PHE* 3.5 26.8 - + + +
223A GLU* 2.8 24.0 + - - -
224A LYS 3.4 13.2 - - - -
225A HIS* 4.4 0.9 - - + -
238A VAL* 4.4 0.6 - - - +
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Residues in contact with ALA 211 (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* 3.8 34.3 - - + +
105A SER* 4.4 3.6 - - - -
175A CYS 3.4 5.2 - - - -
210A TRP* 1.3 76.2 - - - +
212A PHE* 1.3 62.0 + - - +
223A GLU* 3.2 6.1 - - - +
224A LYS 2.9 33.0 + - - +
238A VAL* 4.0 15.7 - - + -
240A LEU* 4.1 13.0 - - + -
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Residues in contact with PHE 212 (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* 4.5 1.0 - - - +
173A LEU* 4.3 13.7 - - + -
174A ILE* 3.2 2.4 - - - +
175A CYS* 2.9 50.9 + - + +
196A LEU* 3.9 29.6 - - + -
198A SER* 3.7 20.4 - - - -
210A TRP* 3.5 24.9 - + + +
211A ALA* 1.3 75.7 - - - +
213A VAL* 1.3 72.0 + - - +
214A GLY* 3.7 27.4 - - - -
220A VAL* 3.6 26.5 - - + -
222A GLY 3.6 7.4 - - - -
223A GLU* 3.8 20.9 - - - -
240A LEU* 4.2 1.4 - - - +
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Residues in contact with VAL 213 (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* 4.1 8.1 - - + -
103A VAL* 3.6 28.0 - - + -
172A VAL* 3.9 12.1 - - + -
173A LEU 3.3 9.0 - - - +
174A ILE* 3.8 12.1 - - + -
212A PHE* 1.3 84.5 - - - +
214A GLY* 1.3 61.9 + - - +
220A VAL* 3.4 2.6 - - - +
221A PHE* 2.8 26.4 + - + -
222A GLY 2.9 16.4 + - - +
240A LEU* 4.1 7.9 - - + -
242A THR* 4.4 10.8 - - + -
244A VAL* 3.8 29.2 - - + -
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Residues in contact with GLY 214 (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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172A VAL* 4.5 1.1 - - - -
173A LEU* 2.6 44.3 + - - +
196A LEU 5.5 0.4 - - - -
212A PHE* 3.7 18.5 - - - -
213A VAL* 1.3 76.2 - - - +
215A ARG* 1.3 61.3 + - - -
219A PRO 3.7 10.3 - - - -
220A VAL* 4.0 2.0 - - - -
221A PHE* 3.9 8.3 - - - -
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Residues in contact with ARG 215 (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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138A GLN* 3.2 33.3 + - - +
170A GLY* 2.9 24.6 + - - +
171A ARG 3.4 6.3 - - - +
172A VAL* 4.1 10.4 - - - +
173A LEU* 5.2 0.7 - - - -
196A LEU* 4.6 7.3 - - - +
214A GLY* 1.3 74.0 - - - -
216A LYS* 1.3 69.7 + - - +
217A GLY 3.1 1.9 + - - -
218A GLY* 3.1 41.7 + - - +
219A PRO* 3.2 17.8 + - + +
221A PHE* 3.4 35.6 - - + -
245A PRO* 4.4 15.4 + - - +
247A SER* 4.7 8.1 - - - +
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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