Contacts of the helix formed by residues 263 - 268 (chain L) in PDB entry 1JH0
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 TRP 263 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169L TYR* 2.9 45.1 + + - -
171L PRO* 4.2 7.6 - - + -
174L MET* 3.6 32.8 - - + -
259L TRP 3.7 12.3 - - - -
260L VAL 3.8 9.6 - - - +
261L ASP 3.0 1.4 - - - -
262L TRP* 1.3 104.7 - + - +
264L GLN* 1.3 62.2 + - - +
265L TRP* 3.3 5.2 - + - -
266L TRP* 3.4 30.6 + + + +
267L VAL* 3.7 7.5 + - - +
90M PHE* 3.7 30.7 - + - -
91M PHE* 4.9 10.9 - + + -
180M PHE* 3.5 24.7 - + + -
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Residues in contact with GLN 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260L VAL 4.7 0.6 + - - +
261L ASP* 3.0 40.8 + - - +
263L TRP* 1.3 74.0 - - - +
265L TRP* 1.3 66.6 + - - +
266L TRP 2.9 3.7 + - - -
267L VAL* 3.0 17.2 + - + +
268L LYS* 2.7 49.5 + - + +
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Residues in contact with TRP 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L TRP* 3.0 71.4 + + - +
263L TRP* 4.4 4.3 - + - +
264L GLN* 1.3 77.4 - - - +
266L TRP* 1.3 97.6 + + + +
268L LYS* 4.0 6.9 + - - +
269L LEU* 3.5 29.8 + - + +
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Residues in contact with TRP 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L TRP* 3.4 20.6 + + + +
264L GLN 2.9 1.6 + - - -
265L TRP* 1.3 121.6 - + + +
267L VAL* 1.3 62.9 + - + +
269L LEU* 3.1 22.3 - - + +
271L TRP* 5.9 2.0 - + - -
272L TRP* 3.0 43.3 + + - -
86M LEU* 3.5 26.1 + - + -
87M ARG* 3.2 29.0 + - - +
89M LEU* 5.5 0.4 - - - +
90M PHE* 5.9 10.2 - + + -
91M PHE* 5.6 5.2 - + - -
850M BCL 6.5 1.3 - - + -
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Residues in contact with VAL 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L TRP 3.7 4.2 + - - +
264L GLN* 3.1 36.6 - - + +
266L TRP* 1.3 83.6 - - + +
268L LYS* 1.3 70.0 + - + +
269L LEU 3.2 4.5 + - - -
272L TRP* 3.5 3.8 - - - -
273L ALA* 3.7 7.1 - - - +
280L ASN* 3.5 40.8 - - + +
87M ARG* 3.4 41.2 - - + +
91M PHE* 5.1 7.6 - - + -
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Residues in contact with LYS 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264L GLN* 2.7 48.5 + - + +
265L TRP* 4.1 7.7 - - - +
267L VAL* 1.3 92.4 - - + +
269L LEU* 1.3 60.2 + - - +
270L PRO* 3.6 6.9 - - - +
273L ALA* 3.8 21.8 + - + +
280L ASN* 5.0 10.9 + - - +
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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