Contacts of the helix formed by residues 303 - 314 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259C ASP* 4.7 3.1 - - - +
262C ILE* 3.5 3.8 - - - -
302C LEU* 1.3 78.3 - - - +
304C TRP* 1.3 67.1 + - - +
305C ASP* 4.5 3.1 - - + +
306C GLU* 3.0 29.3 + - + +
307C ALA* 2.9 20.6 + - - +
522C HIS* 4.0 27.4 - - + +
690C LYS 5.3 1.1 - - - +
691C HIS* 3.9 27.8 - - + +
692C LEU* 4.3 16.8 - - + -
740C ARG* 4.3 9.4 - - + +
742C TRP* 4.6 8.7 - - + -
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Residues in contact with TRP 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C THR 5.0 0.7 - - - -
179C VAL* 4.8 2.5 - - - -
180C ARG* 3.7 63.0 - - + +
233C GLN* 6.0 6.5 - - + -
259C ASP* 5.1 1.6 + - - +
262C ILE* 3.4 20.1 - - + +
303C VAL* 1.3 72.9 - - - +
305C ASP* 1.3 67.3 + - + +
307C ALA* 3.2 1.5 + - + -
308C GLN* 2.9 65.7 + - + +
522C HIS* 6.4 0.2 - - - -
525C ASP* 6.4 2.2 - - + -
526C GLY* 6.3 1.1 - - - -
529C PHE* 3.5 50.4 - + + -
530C GLU* 5.7 2.2 - - - -
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Residues in contact with ASP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG* 2.8 35.2 + - - +
303C VAL* 3.4 3.3 + - + +
304C TRP* 1.3 82.5 - - + +
306C GLU* 1.3 57.4 + - - +
309C LYS* 2.9 42.0 + - - +
690C LYS* 2.8 32.4 + - - +
691C HIS* 2.7 29.4 + - + +
753C ALA* 4.7 0.5 - - - +
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C LEU* 3.4 17.3 - - + +
303C VAL* 3.0 22.7 + - + +
305C ASP* 1.3 76.7 - - - +
307C ALA* 1.3 57.3 + - - +
309C LYS* 3.3 1.7 + - - +
310C LEU* 2.8 34.9 + - + +
660C LEU* 3.7 20.3 - - + +
691C HIS* 3.5 33.0 + - + +
693C LYS* 2.9 21.7 + - - +
740C ARG* 2.8 44.4 + - - -
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C THR* 2.8 38.4 + - - +
262C ILE* 3.6 24.9 - - + -
302C LEU* 3.8 21.5 - - + +
303C VAL 2.9 15.9 + - - +
304C TRP* 3.6 6.7 - - + +
306C GLU* 1.3 77.2 - - - +
308C GLN* 1.3 56.8 + - - +
310C LEU* 4.3 0.2 - - - -
311C THR* 3.0 15.2 + - - +
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B GLY* 3.6 18.4 + - - +
313B ARG* 2.8 53.3 + - - +
655B ALA 5.3 3.1 - - - +
233C GLN* 5.6 4.0 + - - -
304C TRP* 2.9 57.9 + - + +
307C ALA* 1.3 74.4 - - - +
309C LYS* 1.3 64.1 + - - +
311C THR* 2.6 28.0 + - - +
529C PHE* 3.9 16.0 - - - -
533C LYS* 5.2 2.2 - - - +
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Residues in contact with LYS 309 (chain C).
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* 4.4 31.5 - - + +
312B GLY* 5.2 0.9 - - - -
313B ARG* 3.1 36.1 - - - +
683B TYR* 5.9 0.6 - - - -
305C ASP* 2.9 37.9 + - - +
306C GLU 3.9 1.6 - - - +
308C GLN* 1.3 75.3 - - - +
310C LEU* 1.3 57.3 + - - +
312C GLY* 3.0 6.8 + - - -
313C ARG* 3.0 33.6 + - + +
660C LEU* 3.7 20.0 - - + -
683C TYR* 2.7 29.9 + - - -
687C GLU* 2.5 31.6 + - - +
691C HIS* 4.2 1.3 - - + -
753C ALA* 4.2 2.8 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C THR* 3.5 15.0 - - + +
302C LEU* 4.2 13.9 - - + -
306C GLU* 2.8 19.0 + - + +
307C ALA 3.4 5.8 - - - +
309C LYS* 1.3 73.6 - - - +
311C THR* 1.3 58.9 + - - +
313C ARG* 4.2 1.8 - - + +
314C ASP* 2.7 46.3 + - + +
317C PHE* 3.7 41.1 - - + -
660C LEU* 3.9 32.5 - - + +
661C THR* 3.9 27.8 - - + -
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Residues in contact with THR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B THR* 4.5 5.3 + - - +
312B GLY* 3.1 19.4 + - - -
315B PRO* 5.9 0.9 - - - +
176C ALA* 3.6 24.1 - - + +
178C THR* 3.4 28.9 - - - +
179C VAL* 3.8 11.2 - - + +
307C ALA 3.0 21.4 + - - +
308C GLN* 2.6 21.0 + - + +
310C LEU* 1.3 75.7 - - - +
312C GLY* 1.3 58.2 + - - +
315C PRO* 3.4 26.5 - - - +
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLN* 3.6 17.6 + - - +
309B LYS* 4.8 0.9 - - - -
311B THR* 3.2 26.9 + - - -
312B GLY* 3.2 16.2 - - - -
309C LYS 3.0 7.2 + - - -
311C THR* 1.3 81.5 + - - +
313C ARG* 1.3 63.4 + - - +
314C ASP 3.6 0.2 + - - -
315C PRO* 4.0 6.1 - - - +
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Residues in contact with ARG 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLN* 5.1 2.8 - - - +
305B ASP* 2.9 42.5 + - - +
308B GLN* 2.8 54.2 + - - +
309B LYS* 3.7 34.7 - - - +
533B LYS* 4.8 8.5 + - - -
690B LYS* 5.0 2.4 - - - +
753B ALA* 5.7 1.0 + - - -
309C LYS* 3.0 21.5 + - + +
310C LEU* 4.4 5.4 - - + +
312C GLY* 1.3 76.8 - - - +
314C ASP* 1.3 61.4 + - + +
315C PRO* 3.9 2.1 - - - +
655C ALA 5.7 2.0 + - - -
658C PRO* 4.3 26.8 - - + +
660C LEU* 3.4 31.7 - - + +
661C THR* 5.7 1.6 - - + -
683C TYR* 5.9 4.4 - - - -
687C GLU* 5.5 1.6 + - - -
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Residues in contact with ASP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLN* 5.4 0.9 + - - +
178C THR* 5.1 1.7 + - - +
310C LEU* 2.7 33.7 + - + +
311C THR* 4.7 0.2 - - - -
313C ARG* 1.3 76.8 - - + +
315C PRO* 1.3 66.4 - - - +
316C ASP* 3.0 14.2 + - - +
317C PHE* 3.0 37.3 + - + +
320C ARG* 2.8 47.0 + - - -
661C THR* 5.0 6.4 - - + +
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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