Contacts of the strand formed by residues 333 - 342 (chain B) 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 GLU 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B ARG* 5.3 1.4 - - - +
295B PRO* 3.8 0.7 - - - +
296B LEU* 2.9 44.4 + - + +
297B ALA* 4.4 3.5 + - - +
331B PHE* 3.2 23.5 + - - +
332B PRO* 1.3 74.5 - - - +
334B TYR* 1.3 68.2 + - - +
372B LYS* 3.4 21.3 - - + +
373B MET 3.2 5.8 - - - +
374B VAL* 3.9 26.6 - - + +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B PHE* 3.2 19.5 - + - -
185B PHE* 3.7 27.6 - + - -
266B TYR 2.6 33.2 + - - -
267B ARG* 3.3 10.7 - - - +
269B MET 4.1 9.9 - - - -
293B TRP* 3.5 23.6 - - + -
294B LYS 3.2 6.3 - - - +
295B PRO* 3.8 24.5 - - + -
296B LEU* 4.3 4.7 - - - -
332B PRO* 3.8 26.0 - - + +
333B GLU* 1.3 76.5 - - - +
335B GLU* 1.3 61.5 + - - +
336B LEU 4.0 0.6 + - - -
372B LYS* 3.3 4.0 - - - +
373B MET* 2.8 44.4 + - + +
375B LEU* 3.9 13.2 - - + -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 2.7 29.9 + - + +
293B TRP* 3.4 4.2 - - - -
294B LYS* 2.8 63.4 + - + +
296B LEU* 4.0 18.1 - - + +
334B TYR* 1.3 73.4 - - - +
336B LEU* 1.3 70.5 + - - +
337B GLY* 3.5 2.1 + - - -
369B ARG* 3.1 42.7 + - + +
371B GLY 3.2 14.4 - - - +
372B LYS* 4.4 0.4 - - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.8 34.3 - - + -
152B PHE* 4.8 4.5 - - + -
153B LEU* 4.7 4.3 - - + -
189B PHE* 4.7 9.0 - - + -
196B PHE* 6.2 0.7 - - + -
198B LEU* 4.1 17.0 - - + -
291B PHE* 4.8 1.3 - - + -
292B HIS 3.3 17.5 - - - +
293B TRP* 3.6 36.6 - - + -
335B GLU* 1.3 76.5 - - - +
337B GLY* 1.3 62.5 + - - +
338B PHE* 4.0 25.6 - - + -
369B ARG 3.7 0.5 - - - -
370B VAL* 2.8 31.7 + - + -
371B GLY 2.8 11.3 + - - +
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B PHE* 3.6 0.3 - - - -
292B HIS* 2.7 41.0 + - - +
335B GLU* 3.5 2.5 + - - -
336B LEU* 1.3 74.2 - - - +
338B PHE* 1.3 71.1 + - - -
367B VAL* 3.3 21.5 - - - -
368B GLN 3.2 10.5 - - - -
369B ARG* 4.5 1.1 - - - -
370B VAL 4.5 0.2 - - - -
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Residues in contact with PHE 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.7 22.0 - - + -
147B ILE* 4.5 4.0 - - + -
148B THR* 5.2 0.2 - - + -
152B PHE* 6.0 0.4 - + - -
153B LEU* 3.9 23.3 - - + -
279B LEU* 3.9 30.3 - - + -
289B VAL* 3.7 10.3 - - + -
290B ARG 3.5 2.7 - - - -
291B PHE* 3.5 34.5 - + - -
336B LEU* 4.0 20.6 - - + -
337B GLY* 1.3 81.1 - - - -
339B GLN* 1.3 60.9 + - - +
340B LEU* 3.7 15.9 + - + +
366B PRO 3.7 1.0 - - - +
367B VAL* 3.6 1.9 - - - +
368B GLN* 2.8 38.3 + - + +
370B VAL* 3.6 22.9 - - + -
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B PHE 3.6 0.5 - - - +
289B VAL* 3.2 7.4 - - - -
290B ARG* 2.9 44.8 + - + +
292B HIS* 2.7 32.3 + - - +
337B GLY 4.3 0.2 - - - -
338B PHE* 1.3 69.7 - - - +
340B LEU* 1.3 61.3 + - - +
341B ILE* 3.9 7.8 - - + +
360B ILE* 2.8 47.8 + - + +
361B PRO 3.9 2.8 + - - -
362B GLU* 4.0 5.5 - - - +
365B VAL* 2.8 36.3 + - + +
366B PRO 3.9 4.9 - - - +
367B VAL* 3.8 11.7 - - + -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.8 24.0 - - + -
279B LEU* 3.6 28.7 - - + -
287B THR* 4.2 11.7 - - + -
288B PHE 3.5 3.4 - - - +
289B VAL* 3.7 20.9 - - + -
338B PHE* 3.7 15.6 + - + +
339B GLN* 1.3 73.6 - - - +
341B ILE* 1.3 62.0 + - - +
342B PRO* 4.1 4.9 - - - +
365B VAL* 3.6 17.3 - - - +
366B PRO 4.6 1.4 + - - -
368B GLN* 3.4 32.1 - - + +
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B THR* 5.7 1.1 - - + -
287B THR* 3.8 4.2 - - - +
288B PHE* 2.8 50.9 + - + +
289B VAL* 5.2 1.6 - - - +
290B ARG* 5.3 0.4 - - + +
339B GLN 3.9 14.8 - - - +
340B LEU* 1.3 81.0 - - - +
342B PRO* 1.3 79.8 - - + +
345B ASP* 3.5 22.2 - - + +
349B PHE* 4.2 11.4 - - + -
353B LEU* 4.0 22.4 - - + -
360B ILE* 3.8 28.7 - - + -
365B VAL* 4.1 21.3 - - + -
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Residues in contact with PRO 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ALA 5.5 0.2 - - - +
287B THR* 4.6 7.8 - - + +
288B PHE* 3.9 1.0 - - - -
340B LEU 4.1 5.4 - - - +
341B ILE* 1.3 96.4 - - + +
343B GLU* 1.3 65.3 + - - +
344B GLU* 3.4 25.6 - - - +
345B ASP* 2.9 39.4 + - - +
346B GLU 3.9 0.9 + - - -
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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