Contacts of the helix formed by residues 299 - 307 (chain D) in PDB entry 3COG
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 GLN 299 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D SER* 5.2 9.2 + - - +
165D LYS* 3.9 5.8 - - - +
166D VAL* 3.0 58.5 + - + +
297D HIS* 3.0 19.6 + - - +
298D PRO* 1.3 99.6 + - - +
300D HIS* 1.3 63.7 + - - +
301D GLU 3.2 3.4 - - - -
302D LEU* 3.1 18.4 + - + -
303D VAL* 3.0 24.0 + - - +
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Residues in contact with HIS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.7 5.6 - + - -
292D PRO 2.8 26.7 + - - +
293D GLY* 3.3 27.4 - - - -
294D LEU 3.3 14.9 + - - +
295D PRO* 3.6 26.9 - - + +
297D HIS* 3.0 19.8 + - + +
298D PRO 3.5 0.8 + - - -
299D GLN* 1.3 76.7 - - - +
301D GLU* 1.3 78.3 + - + +
303D VAL* 3.4 4.3 - - - +
304D LYS* 3.2 46.2 + - + +
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Residues in contact with GLU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D GLN 3.2 1.2 - - - -
300D HIS* 1.3 83.5 - - + +
302D LEU* 1.3 68.1 + - - +
304D LYS* 3.0 50.2 + - - +
305D ARG* 3.1 30.9 + - - +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 4.0 22.7 - - + +
167D ILE 4.0 0.9 - - - -
168D ASP* 3.8 50.3 - - + +
299D GLN* 3.1 20.5 + - + +
301D GLU* 1.3 75.1 - - - +
303D VAL* 1.3 64.2 + - - +
305D ARG* 2.9 47.1 + - + +
306D GLN* 2.9 31.1 + - + +
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.0 18.8 - - + -
166D VAL* 4.0 22.0 - - + -
191D MET* 5.8 1.1 - - + -
292D PRO* 3.9 30.1 - - + +
297D HIS* 5.0 0.2 - - - +
299D GLN 3.0 24.4 + - - +
300D HIS 3.4 8.3 - - - +
302D LEU* 1.3 76.2 - - - +
304D LYS* 1.3 55.4 + - - +
306D GLN* 4.5 2.5 - - - -
307D CYS* 2.9 53.5 + - + +
309D GLY 4.9 0.4 - - - +
310D CYS* 4.1 15.9 - - - -
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Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLY* 3.6 29.4 - - - +
11D PHE* 3.4 39.5 - - + -
12D LEU* 3.1 27.5 + - - +
300D HIS* 3.2 29.8 + - + +
301D GLU* 3.0 48.8 + - - +
303D VAL* 1.3 80.4 - - - +
305D ARG* 1.3 60.4 + - + +
307D CYS 3.3 1.4 - - - +
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Residues in contact with ARG 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.1 24.6 - - - +
168D ASP* 5.2 3.8 + - - -
201D LEU* 5.4 1.7 - - - +
301D GLU* 3.1 28.4 + - - +
302D LEU* 2.9 42.5 + - + +
304D LYS* 1.3 79.1 - - + +
306D GLN* 1.3 58.1 + - + +
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.6 12.8 - - - +
15D PHE* 5.9 0.3 - - - -
158D THR* 4.0 3.6 + - - -
166D VAL* 3.9 17.0 - - - +
167D ILE 2.8 22.4 + - - +
168D ASP* 3.8 4.2 - - - +
169D ILE* 3.1 35.9 + - - +
170D GLU 4.7 0.7 + - - -
195D PHE 4.3 0.3 - - - +
196D GLN* 3.5 25.3 + - - +
197D ARG 4.9 0.7 + - - -
201D LEU* 3.8 30.6 - - + +
302D LEU* 2.9 29.0 + - + +
303D VAL* 4.5 0.2 - - - -
305D ARG* 1.3 76.9 - - + +
307D CYS* 1.3 71.3 + - - +
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Residues in contact with CYS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.5 6.6 - - - -
12D LEU* 3.0 23.3 + - - -
159D PRO* 6.3 0.4 - - - -
166D VAL* 6.3 0.7 - - - -
191D MET* 4.2 11.4 - - - -
195D PHE 3.1 12.8 - - - +
196D GLN* 3.3 30.1 - - - -
303D VAL* 2.9 29.6 + - + +
304D LYS 3.3 5.5 - - - +
305D ARG 3.6 0.4 - - - -
306D GLN* 1.3 86.5 - - - +
308D THR* 1.3 61.3 + - - +
309D GLY 3.4 17.7 - - - +
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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