Contacts of the helix formed by residues 300 - 307 (chain A) in PDB entry 2H1H
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 PRO 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ARG 3.9 5.2 - - - +
299A ALA* 1.3 84.1 - - + +
301A GLY* 1.3 64.3 + - - +
302A ASN 2.9 1.6 + - - -
303A GLU 3.0 13.2 + - - +
306A GLN* 3.0 50.8 - - + +
307A LEU* 3.9 13.2 - - + -
43B GLN* 3.6 32.1 - - + +
46B SER* 5.2 9.0 - - - +
245B GLU* 4.0 9.9 - - - +
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Residues in contact with GLY 301 (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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299A ALA 3.3 0.8 + - - -
300A PRO* 1.3 71.6 - - - +
302A ASN* 1.3 69.6 + - - +
303A GLU* 3.0 10.4 + - - +
306A GLN* 3.8 7.9 + - - -
42B ALA* 3.8 36.6 + - - +
43B GLN* 4.7 1.2 - - - +
46B SER* 5.7 0.6 + - - -
54B VAL* 5.7 3.3 - - - +
56B PRO* 4.4 9.3 - - - +
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Residues in contact with ASN 302 (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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280A GLY* 3.2 40.1 - - - +
281A PRO* 3.4 9.0 - - + +
298A ARG* 5.5 5.2 - - - +
299A ALA 2.9 14.9 + - - +
301A GLY* 1.3 77.4 - - - +
303A GLU* 1.3 60.0 + - - +
53B ARG* 3.3 31.6 + - - +
54B VAL* 2.9 31.6 + - - +
56B PRO* 3.4 19.2 - - + +
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Residues in contact with GLU 303 (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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299A ALA* 3.5 6.7 + - - +
300A PRO 3.0 6.1 + - - +
301A GLY 3.9 5.6 - - - +
302A ASN* 1.3 78.8 - - - +
304A LEU* 1.3 56.6 + - - +
305A SER* 3.0 16.6 + - - +
306A GLN* 2.5 70.6 + - - +
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Residues in contact with LEU 304 (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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191A ASP 3.3 22.6 + - - +
192A LYS* 3.1 32.1 - - - +
193A HIS 3.4 16.8 - - - +
194A TRP* 3.5 20.8 + - + +
195A PRO* 3.7 7.1 - - + +
198A HIS* 3.9 0.2 - - - -
278A VAL* 3.9 27.8 - - + +
279A TYR 3.9 8.5 - - - +
280A GLY* 3.9 18.1 - - - +
299A ALA* 3.7 18.8 - - + +
302A ASN 4.0 1.0 + - - -
303A GLU* 1.3 73.2 - - - +
305A SER* 1.3 61.0 + - - +
306A GLN 2.9 0.2 - - - -
307A LEU* 3.0 22.5 + - + +
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Residues in contact with SER 305 (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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195A PRO* 3.8 21.6 - - - +
198A HIS* 3.2 20.2 + - - -
303A GLU* 3.6 25.8 + - - +
304A LEU* 1.3 77.8 - - - +
306A GLN* 1.3 62.6 + - - +
307A LEU 3.4 0.2 - - - -
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Residues in contact with GLN 306 (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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198A HIS* 5.8 0.2 - - - -
300A PRO* 3.0 48.2 - - + +
301A GLY* 3.8 7.0 + - - -
303A GLU* 2.5 46.1 + - + +
305A SER* 1.3 81.7 + - - +
307A LEU* 1.3 59.1 + - - -
308A THR* 3.5 12.3 + - - +
43B GLN* 4.3 12.6 + - - +
243B SER* 6.1 4.0 - - - -
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Residues in contact with LEU 307 (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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194A TRP* 3.0 32.6 + - + +
198A HIS* 3.6 14.1 + - - -
278A VAL* 3.6 32.3 - - + -
297A CYS* 3.8 22.0 - - - -
298A ARG 4.6 1.1 - - - +
299A ALA* 3.7 15.9 - - + -
300A PRO* 3.9 16.3 - - + +
303A GLU 3.7 1.0 + - - -
304A LEU* 3.0 15.1 + - + +
305A SER 5.0 0.2 - - - -
306A GLN* 1.3 76.9 - - - +
308A THR* 1.3 61.7 + - - +
311A ALA* 3.9 19.7 - - + -
312A VAL* 3.6 18.8 - - + -
315A PHE* 5.4 0.7 - - + -
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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