Contacts of the strand formed by residues 367 - 377 (chain A) in PDB entry 1GGE
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 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A HIS* 3.5 42.8 - - + +
294A LYS* 4.8 15.0 - - - +
337A GLY* 3.5 35.2 - - - -
338A PHE 3.6 3.8 - - - -
339A GLN* 3.8 7.6 - - + -
362A GLU* 3.7 24.5 + - - +
366A PRO* 1.3 75.6 - - - +
368A GLN* 1.3 60.0 + - - +
369A ARG* 3.7 16.7 + - - +
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Residues in contact with GLN 368 (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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142A LYS* 4.0 19.9 + - - -
144A LEU* 4.0 17.0 - - - +
147A ILE* 4.9 2.9 - - - +
337A GLY* 3.1 3.5 - - - -
338A PHE* 2.8 39.3 + - + +
340A LEU* 3.3 29.1 - - + +
366A PRO 3.5 3.7 + - - +
367A VAL* 1.3 71.7 - - - +
369A ARG* 1.3 74.1 + - - +
370A VAL* 3.5 6.6 + - + +
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Residues in contact with ARG 369 (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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141A TYR* 3.8 16.7 - - + +
142A LYS* 5.9 3.5 - - - +
144A LEU* 5.7 1.0 - - - +
294A LYS* 4.3 15.4 - - - +
335A GLU* 3.0 37.0 - - - +
336A LEU 4.0 4.3 - - - -
337A GLY* 4.4 1.8 - - - -
367A VAL* 4.0 15.0 + - + +
368A GLN* 1.3 86.5 - - - +
370A VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 4.4 0.2 - - + -
140A PRO* 3.3 5.5 - - - +
141A TYR* 2.8 25.9 + - - +
142A LYS* 4.4 2.9 + - - +
144A LEU* 3.7 28.6 - - + +
153A LEU* 3.7 20.4 - - + -
336A LEU* 2.8 31.2 + - + +
338A PHE* 3.6 39.0 - - + +
368A GLN* 3.7 13.9 - - + +
369A ARG* 1.3 79.0 - - - +
371A GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 371 (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 PHE* 3.8 12.3 - - - -
139A GLN 3.3 13.0 - - - -
140A PRO* 3.8 2.9 - - - -
141A TYR* 3.6 14.6 - - - -
335A GLU* 3.3 10.2 - - - +
336A LEU* 2.9 23.3 + - - +
370A VAL* 1.3 84.0 - - - +
372A LYS* 1.3 61.5 + - - -
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Residues in contact with LYS 372 (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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137A TYR* 3.9 2.3 - - - +
138A PHE* 3.3 6.1 - - - -
139A GLN* 3.0 36.5 + - + +
141A TYR* 3.8 22.3 - - + +
296A LEU* 3.7 26.1 - - + +
333A GLU* 3.0 25.8 + - - +
334A TYR 3.5 8.3 - - - +
371A GLY* 1.3 76.0 - - - -
373A MET* 1.3 70.7 + - - +
374A VAL* 4.1 13.3 + - + +
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Residues in contact with MET 373 (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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137A TYR 3.4 9.9 - - - +
138A PHE* 4.2 4.5 - - + +
162A VAL* 3.7 13.2 - - + -
164A VAL* 3.7 14.8 - - + -
185A PHE* 3.8 21.1 - - + -
187A THR* 3.7 33.2 - - - +
189A PHE* 5.1 0.2 - - - -
293A TRP* 3.4 43.5 - - + -
332A PRO 3.9 0.3 - - - +
333A GLU* 3.2 6.4 - - - +
334A TYR* 2.9 42.9 + - + +
372A LYS* 1.3 75.9 - - - +
374A VAL* 1.3 63.9 + - - +
375A LEU* 3.9 13.2 - - + -
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Residues in contact with VAL 374 (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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136A GLY* 3.0 2.8 - - - -
137A TYR* 2.9 72.1 + - + +
331A PHE* 3.8 32.8 - - + -
332A PRO 3.6 4.0 - - - +
333A GLU* 4.1 20.6 - - + +
372A LYS* 4.1 19.3 - - + +
373A MET* 1.3 77.6 - - - +
375A LEU* 1.3 68.2 + - - +
376A ASN* 3.7 2.2 + - + -
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Residues in contact with LEU 375 (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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134A ALA* 4.4 11.0 - - + +
135A HIS 3.4 11.0 - - - +
136A GLY* 4.1 3.8 - - - +
162A VAL* 3.9 9.6 - - + -
164A VAL* 3.7 32.8 - - + -
166A PHE* 3.9 28.9 - - + -
322A LEU* 5.1 0.4 - - + -
326A ILE* 3.7 9.2 - - + +
331A PHE* 3.1 10.3 - - - +
332A PRO* 2.9 54.5 + - + +
334A TYR* 4.0 12.6 - - + -
373A MET* 3.9 15.0 - - + -
374A VAL* 1.3 76.8 - - - +
376A ASN* 1.3 58.8 + - - +
377A ARG 3.8 0.7 - - - -
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Residues in contact with ASN 376 (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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57A ALA* 5.2 1.7 - - - +
60A THR* 3.7 28.8 + - + +
61A ARG 5.4 3.4 + - - -
62A ASN* 5.1 3.8 + - - -
65A LEU* 5.2 0.9 - - - +
135A HIS 3.0 2.8 + - - +
136A GLY* 3.7 14.0 - - - -
137A TYR* 3.5 31.4 - - - -
326A ILE* 3.7 8.3 - - - +
331A PHE* 3.5 41.0 - - + -
374A VAL* 4.3 3.6 - - + -
375A LEU* 1.3 73.9 - - - +
377A ARG* 1.3 69.3 + - - +
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Residues in contact with ARG 377 (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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53A GLY* 3.4 9.6 - - - +
54A SER* 3.4 29.6 - - - +
57A ALA* 3.6 30.5 + - + -
60A THR* 3.9 28.1 + - + -
65A LEU* 3.7 42.7 - - + +
72A ARG* 3.8 9.5 - - - +
134A ALA* 3.6 2.7 - - - +
135A HIS* 2.7 38.5 + - + +
326A ILE* 3.7 8.7 - - + +
375A LEU 3.8 0.4 - - - -
376A ASN* 1.3 84.0 - - - +
378A ASN* 1.3 83.3 + - - +
379A PRO* 4.0 6.1 - - - +
380A ASP* 3.6 21.0 + - - -
385A GLU* 4.7 0.6 + - - -
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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