Contacts of the helix formed by residues 303 - 314 (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 VAL 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ASP* 4.8 3.1 - - - +
262B ILE* 3.5 4.0 - - - -
301B SER 5.4 0.2 - - - +
302B LEU* 1.3 79.8 - - - +
304B TRP* 1.3 64.8 + - - +
305B ASP* 4.6 2.2 - - + +
306B GLU* 3.0 26.7 + - + +
307B ALA* 3.0 19.6 + - - +
522B HIS* 3.9 28.3 - - + +
690B LYS 5.4 0.4 - - - +
691B HIS* 4.0 26.5 - - + -
692B LEU* 4.2 17.7 - - + -
740B ARG* 4.1 7.9 - - - +
742B TRP* 4.6 8.3 - - + -
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Residues in contact with TRP 304 (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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178B THR 5.1 0.4 - - - -
179B VAL* 4.8 2.5 - - - -
180B ARG* 3.7 64.4 - - + +
233B GLN* 5.9 7.6 - - + -
259B ASP* 5.0 1.8 + - - +
262B ILE* 3.4 17.9 - - + +
303B VAL* 1.3 72.9 - - - +
305B ASP* 1.3 62.5 + - + +
307B ALA* 3.2 2.2 + - + -
308B GLN* 2.9 66.2 + - + +
522B HIS* 6.3 0.6 - - - -
525B ASP* 6.4 1.8 - - + -
526B GLY* 6.3 0.7 - - - -
529B PHE* 3.4 57.2 - + + -
530B GLU* 5.7 2.5 - - - -
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Residues in contact with ASP 305 (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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303B VAL* 3.4 2.9 - - + +
304B TRP* 1.3 83.9 - - + +
306B GLU* 1.3 57.3 + - - +
309B LYS* 3.0 34.0 + - - +
690B LYS* 2.7 35.6 + - - +
691B HIS* 2.9 25.0 + - + +
753B ALA* 4.8 0.2 - - - +
313C ARG* 2.9 40.3 + - - +
655C ALA* 6.1 1.2 - - - +
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Residues in contact with GLU 306 (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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302B LEU* 3.3 19.2 - - + +
303B VAL* 3.0 21.0 + - + +
304B TRP 3.2 0.2 - - - -
305B ASP* 1.3 75.8 - - - +
307B ALA* 1.3 58.5 + - - +
309B LYS* 3.4 1.4 + - - +
310B LEU* 2.8 34.8 + - + +
660B LEU* 3.8 18.7 - - + +
691B HIS* 3.5 32.7 + - + +
693B LYS* 2.8 27.5 + - - +
740B ARG* 2.7 40.6 + - - -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 2.9 37.8 + - - +
262B ILE* 3.8 24.7 - - + -
302B LEU* 3.8 22.2 - - + +
303B VAL 3.0 12.8 + - - +
304B TRP* 3.6 10.1 - - + +
306B GLU* 1.3 76.9 - - - +
308B GLN* 1.3 63.1 + - - +
310B LEU* 3.3 1.0 + - - -
311B THR* 3.0 10.6 + - - +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLN* 5.7 1.2 + - - -
304B TRP* 2.9 59.8 + - + +
305B ASP* 5.2 0.2 - - - -
307B ALA* 1.3 76.0 - - - +
309B LYS* 1.3 61.7 + - - +
311B THR* 2.6 27.7 + - - +
529B PHE* 3.6 17.2 - - - -
533B LYS* 4.7 4.9 - - - +
312C GLY* 3.6 21.4 + - - +
313C ARG* 2.8 53.6 + - - +
655C ALA 5.2 3.6 - - - +
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Residues in contact with LYS 309 (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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305B ASP* 3.0 25.6 + - - +
306B GLU 4.0 0.9 - - - +
308B GLN* 1.3 76.3 - - - +
310B LEU* 1.3 57.6 + - - +
312B GLY* 3.0 6.1 + - - -
313B ARG* 2.9 42.4 + - + +
660B LEU* 3.8 18.2 - - + -
683B TYR* 2.8 29.7 + - - -
687B GLU* 2.6 33.2 + - - +
753B ALA* 4.4 3.2 + - - -
309C LYS* 4.4 25.9 - - + +
312C GLY* 5.2 2.0 - - - -
313C ARG* 3.7 32.7 - - - +
683C TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 310 (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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178B THR* 3.5 15.7 - - + +
302B LEU* 4.3 13.0 - - + -
306B GLU* 2.8 19.8 + - + +
307B ALA 3.5 5.2 - - - +
309B LYS* 1.3 73.1 - - - +
311B THR* 1.3 61.0 + - - +
313B ARG* 4.2 1.3 - - + +
314B ASP* 2.8 45.5 + - + +
317B PHE* 3.6 40.4 - - + -
660B LEU* 3.8 40.9 - - + +
661B THR* 4.1 19.7 - - + -
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Residues in contact with THR 311 (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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176B ALA* 3.6 24.2 - - + +
178B THR* 3.2 35.7 - - - +
179B VAL* 3.7 12.1 - - + +
307B ALA 3.0 10.6 + - - +
308B GLN* 2.6 20.8 + - - +
310B LEU* 1.3 76.2 - - - +
312B GLY* 1.3 58.8 + - - +
315B PRO* 3.5 25.7 - - - +
311C THR* 4.5 5.2 + - - +
312C GLY* 3.2 19.1 + - - -
315C PRO* 6.1 0.2 - - - +
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Residues in contact with GLY 312 (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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309B LYS 3.0 6.6 + - - -
311B THR* 1.3 78.3 - - - +
313B ARG* 1.3 63.7 + - - +
314B ASP 3.4 0.6 + - - -
315B PRO* 4.0 5.9 - - - +
308C GLN* 3.6 19.9 + - - +
309C LYS* 4.7 1.1 - - - -
311C THR* 3.1 26.5 + - - -
312C GLY* 3.2 20.0 - - - -
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 2.9 23.3 + - + +
310B LEU* 4.4 4.9 - - + +
312B GLY* 1.3 76.2 - - - +
314B ASP* 1.3 61.9 + - + +
315B PRO* 4.0 1.5 - - - +
655B ALA 5.7 3.8 - - - -
658B PRO* 4.0 24.0 - - + +
660B LEU* 3.4 29.8 - - + -
661B THR* 5.8 0.7 - - + -
683B TYR* 5.9 4.6 - - - -
687B GLU* 5.6 0.2 + - - -
233C GLN* 5.3 4.2 - - - +
305C ASP* 2.8 35.9 + - - +
308C GLN* 2.8 47.2 + - - +
309C LYS* 3.1 39.1 - - - +
533C LYS* 5.3 5.2 + - - -
690C LYS* 5.1 1.8 - - - +
753C ALA* 5.6 1.4 + - - -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 5.1 1.4 + - - +
310B LEU* 2.8 29.3 + - + +
311B THR* 4.7 0.2 - - - -
313B ARG* 1.3 75.8 - - + +
315B PRO* 1.3 69.5 - - - +
316B ASP* 3.0 14.4 + - - +
317B PHE* 3.0 39.0 + - + +
320B ARG* 2.8 47.2 + - - -
661B THR* 5.1 8.4 - - + +
233C GLN* 5.3 1.3 + - - +
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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