Contacts of the helix formed by residues 310 - 316 (chain A) in PDB entry 3GG0
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 GLY 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLU* 3.4 11.0 - - - -
304A PHE* 3.5 16.7 - - - -
305A GLY 5.5 0.4 - - - -
308A TYR 3.0 9.5 + - - -
309A SER* 1.3 74.5 - - - +
311A LEU* 1.3 63.0 + - - -
312A SER 3.3 2.7 - - - -
313A LEU* 3.2 19.8 + - - +
309B SER 3.8 1.0 - - - -
310B GLY* 3.7 8.8 - - - +
311B LEU 4.8 1.1 - - - -
312B SER* 3.7 13.5 - - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.8 13.4 - - + -
310A GLY* 1.3 68.4 - - - -
312A SER* 1.3 61.6 + - - +
313A LEU 3.2 2.8 + - - -
314A LEU* 3.5 26.3 + - + +
344A SER 4.3 1.1 - - - +
345A VAL* 4.3 24.7 - - + -
348A CYS* 3.6 36.1 - - + -
349A CYS* 6.4 0.4 - - - -
304B PHE* 6.3 0.7 - - + -
310B GLY* 4.0 7.9 - - - -
311B LEU* 3.8 36.0 - - + +
341B ILE* 3.6 37.6 - - + +
344B SER* 4.7 3.1 - - - +
345B VAL* 5.0 3.6 - - + -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER* 5.1 1.0 + - - -
310A GLY 4.7 0.7 + - - -
311A LEU* 1.3 75.8 - - - +
313A LEU* 1.3 65.0 + - - +
314A LEU 3.1 2.9 - - - -
315A THR* 3.1 28.5 + - - -
316A ARG* 4.3 6.6 + - - +
304B PHE* 6.4 0.2 - - - -
305B GLY* 3.2 35.5 + - - -
307B GLY 3.6 13.1 + - - -
308B TYR* 4.6 0.7 - - - -
309B SER 2.7 28.8 + - - -
310B GLY* 4.9 0.8 - - - -
328B LEU* 5.3 3.4 - - - -
341B ILE* 4.7 5.8 - - - -
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 5.3 4.3 - - + -
278A VAL* 4.8 5.4 - - + -
279A ILE* 3.8 20.4 - - + -
282A PHE* 3.7 32.5 - - + -
301A ILE* 4.3 24.5 - - + -
304A PHE* 5.1 6.5 - - + -
309A SER* 4.5 11.4 - - - +
310A GLY 3.2 16.3 + - - +
311A LEU 3.2 0.4 - - - -
312A SER* 1.3 81.1 + - - +
314A LEU* 1.3 62.4 + - + +
315A THR 3.1 0.7 - - - -
316A ARG* 3.0 24.4 + - - +
317A PHE* 3.4 40.0 + - + +
319A PRO* 5.9 0.4 - - + -
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Residues in contact with LEU 314 (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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304A PHE* 5.6 2.9 - - + -
310A GLY 5.4 0.2 - - - +
311A LEU* 3.5 30.1 - - + +
312A SER 3.1 0.8 - - - -
313A LEU* 1.3 80.2 - - + +
315A THR* 1.3 58.5 + - - +
316A ARG 3.2 0.4 - - - -
317A PHE 3.3 7.2 - - - +
318A GLN* 2.7 32.7 + - + -
319A PRO* 3.9 17.7 - - + -
322A ILE* 4.0 17.7 - - + -
348A CYS* 3.8 29.2 - - - -
349A CYS* 5.6 2.0 - - - -
352A LEU* 3.8 14.1 - - + -
354A ILE* 3.8 26.2 - - + -
337B THR* 3.6 7.8 - - + +
341B ILE* 4.0 9.2 - - + -
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Residues in contact with THR 315 (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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312A SER* 3.1 16.2 + - - -
313A LEU 3.1 0.6 - - - -
314A LEU* 1.3 80.4 - - - +
316A ARG* 1.3 81.8 + - - +
318A GLN* 4.5 2.9 + - - -
327B GLU* 5.5 6.7 - - + +
328B LEU* 3.7 23.5 - - + +
337B THR* 4.9 4.0 - - - -
338B LYS* 4.6 21.8 - - + +
341B ILE* 3.7 8.2 - - - +
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Residues in contact with ARG 316 (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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282A PHE* 4.2 36.7 - - + -
312A SER 4.5 3.4 + - - -
313A LEU* 3.0 19.2 + - - +
315A THR* 1.3 105.0 - - - +
317A PHE* 1.3 74.1 + - + +
318A GLN* 4.7 0.7 - - - -
305B GLY 4.1 7.1 + - - -
306B ALA* 5.0 0.4 - - - +
307B GLY* 2.9 44.3 + - - +
327B GLU* 4.9 18.0 + - - +
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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