Contacts of the helix formed by residues 345 - 350 (chain B) in PDB entry 2XGZ
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 LYS 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ASP* 3.0 27.3 + - - +
321B ARG* 5.9 1.8 - - - +
325B THR* 3.1 15.1 + - - +
343B LEU* 3.7 10.8 - - + +
344B LEU* 1.3 72.6 - - - +
346B VAL* 1.3 67.3 + - - +
347B ASN* 3.2 2.0 - - - +
348B GLN* 2.9 51.1 + - + +
349B ILE 3.7 2.4 + - - -
372B SER* 3.8 15.9 - - - -
373B HIS 4.1 1.8 - - - +
374B ARG* 3.8 33.4 - - - +
1440B PEP 2.6 46.7 + - - -
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 5.3 7.9 - - + -
111B LEU* 4.0 23.9 - - + +
115B LEU* 4.8 11.7 - - + -
344B LEU* 3.8 8.9 + - + +
345B LYS* 1.3 71.6 - - - +
347B ASN* 1.3 60.3 + - + +
348B GLN 3.3 0.3 + - - -
349B ILE* 3.4 5.5 + - - +
350B GLY* 2.9 25.5 + - - -
351B THR 4.2 2.4 + - - +
352B LEU* 5.4 2.2 - - + -
355B SER* 3.3 24.9 + - - +
371B VAL* 6.0 0.2 - - + -
372B SER 5.2 1.4 + - - -
382B PHE* 5.2 6.1 - - + -
383B ILE* 4.7 17.5 - - + +
386B LEU* 3.4 33.2 - - + -
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Residues in contact with ASN 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 4.4 5.3 - - + +
35B PRO* 3.3 25.8 + - + +
36B SER 2.9 30.7 + - - -
37B GLY* 3.4 10.9 - - - -
45B ALA* 4.2 11.4 - - - +
47B GLU* 4.7 1.8 + - - +
107B ALA* 4.3 10.9 - - + +
111B LEU* 3.3 26.5 - - + -
345B LYS* 4.2 1.7 - - - +
346B VAL* 1.3 79.3 - - - +
348B GLN* 1.3 61.3 + - - +
349B ILE 3.3 0.2 - - - -
350B GLY* 4.0 6.3 + - - +
374B ARG* 2.8 31.7 + - - +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 3.2 33.7 + - + +
45B ALA 2.9 28.1 + - - +
320B ASP* 4.6 4.6 + - - +
321B ARG* 4.0 7.3 - - - +
324B VAL* 3.3 42.1 - - - +
325B THR* 2.8 25.4 + - - +
343B LEU 4.9 1.2 - - - +
345B LYS* 2.9 45.4 + - + +
347B ASN* 1.3 81.1 + - - +
349B ILE* 1.3 59.1 + - - +
374B ARG* 4.2 11.5 - - - +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B HIS 5.9 0.9 - - - +
45B ALA* 3.5 7.8 - - + +
102B LYS* 2.8 30.7 + - - +
324B VAL 5.8 0.2 - - - +
325B THR* 3.5 34.1 - - + +
326B ASN* 4.7 4.7 - - - +
327B PRO* 3.7 22.7 - - + -
345B LYS 3.7 0.2 + - - -
346B VAL 3.4 3.3 + - - +
348B GLN* 1.3 81.3 - - - +
350B GLY* 1.3 59.5 + - - +
351B THR 3.6 7.4 - - - +
354B GLU* 3.6 33.0 - - + +
355B SER* 3.3 35.4 - - - +
358B ALA* 6.1 0.2 - - + -
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 4.5 2.0 - - - -
102B LYS* 3.8 11.2 - - - -
107B ALA* 4.6 4.7 - - - -
110B ILE* 3.4 3.8 - - - +
111B LEU* 3.3 39.6 + - - -
346B VAL 2.9 11.7 + - - -
347B ASN 4.0 7.4 - - - -
348B GLN 3.8 0.4 - - - -
349B ILE* 1.3 77.3 - - - +
351B THR* 1.3 67.2 + - - +
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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