Contacts of the helix formed by residues 251 - 263 (chain A) in PDB entry 4Z4H
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 THR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A PRO 3.7 2.6 + - - +
250A LEU* 1.3 74.8 - - - +
252A ASP* 1.3 61.2 + - - +
253A SER* 3.3 11.1 + - - -
254A GLN* 2.9 39.3 + - - +
255A ARG* 2.8 26.6 + - - +
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Residues in contact with ASP 252 (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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250A LEU 3.8 0.2 + - - -
251A THR* 1.3 74.5 - - - +
253A SER* 1.3 80.0 + - - +
255A ARG* 3.4 35.6 + - - +
256A VAL* 3.0 32.4 + - - +
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Residues in contact with SER 253 (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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251A THR* 3.0 9.6 - - - -
252A ASP* 1.3 89.0 + - - +
254A GLN* 1.3 59.7 + - - +
256A VAL* 2.9 23.0 - - - +
257A LYS* 3.4 10.0 + - - +
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Residues in contact with GLN 254 (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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238A LEU* 3.4 27.9 + - + +
240A PHE* 3.4 34.4 - - - -
250A LEU* 3.7 20.2 - - + +
251A THR* 2.9 39.8 + - - +
253A SER* 1.3 77.3 - - - +
255A ARG* 1.3 64.4 + - - +
256A VAL 3.2 0.2 - - - -
257A LYS* 3.4 1.9 + - - -
258A PHE* 3.1 21.2 + - - +
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Residues in contact with ARG 255 (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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250A LEU* 4.1 25.5 + - + +
251A THR 2.8 13.2 + - - +
252A ASP* 3.4 41.5 + - - +
254A GLN* 1.3 73.3 - - - +
256A VAL* 1.3 52.4 + - - +
258A PHE* 4.0 3.7 - - + +
259A THR* 2.5 42.7 + - - +
284A VAL* 4.3 13.3 + - + +
285A THR 3.5 21.7 - - - -
286A ARG* 3.8 41.4 + - - +
326A PRO* 4.6 11.2 - - + -
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Residues in contact with VAL 256 (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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252A ASP 3.0 17.1 + - - +
253A SER* 2.9 24.2 - - - +
255A ARG* 1.3 77.0 - - - +
257A LYS* 1.3 77.2 + - + +
259A THR* 3.1 6.2 + - - -
260A LYS* 3.0 48.4 + - + +
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.2 32.3 - - + +
238A LEU* 4.1 13.2 - - + +
253A SER 3.7 12.8 - - - +
254A GLN* 3.4 5.5 + - - +
256A VAL* 1.3 84.4 - - + +
258A PHE* 1.3 62.5 + - - +
260A LYS* 3.4 9.5 + - - +
261A GLU* 3.3 33.3 + - + +
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Residues in contact with PHE 258 (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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230A VAL* 4.0 4.5 - - + -
233A PHE* 3.8 26.2 - + - -
234A VAL* 3.4 43.1 - - + -
237A VAL* 4.0 11.7 - - + -
238A LEU* 4.2 13.0 - - + +
250A LEU* 5.0 11.2 - - + -
254A GLN 3.1 17.9 + - - +
255A ARG* 4.0 4.7 - - - +
257A LYS* 1.3 75.6 - - - +
259A THR* 1.3 65.8 + - - +
261A GLU* 3.2 2.1 + - - +
262A ILE* 3.2 42.2 + - + +
284A VAL* 3.8 32.8 - - + -
326A PRO* 5.2 0.9 - - + -
328A LEU* 4.0 9.9 - - + -
341A LEU* 4.4 9.4 - - + -
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ARG* 2.5 27.2 + - - +
256A VAL* 3.1 9.0 + - - -
258A PHE* 1.3 76.9 - - - +
260A LYS* 1.3 64.4 + - + +
262A ILE* 4.0 0.3 - - - +
263A LYS* 3.0 59.4 + - + +
283A ASN* 4.1 5.2 - - - +
284A VAL* 3.3 43.2 + - + +
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Residues in contact with LYS 260 (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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256A VAL* 3.0 39.5 + - + +
257A LYS* 3.7 9.0 - - - +
259A THR* 1.3 78.5 - - + +
261A GLU* 1.3 66.1 + - + +
263A LYS* 4.4 9.7 + - - +
354A LYS* 3.4 22.3 + - - +
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Residues in contact with GLU 261 (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 GLY* 4.9 5.4 - - - +
196A ARG* 3.0 31.0 + - - -
225A TYR* 4.3 3.6 + - - -
233A PHE* 4.0 7.7 - - + -
237A VAL* 3.7 34.8 - - + -
257A LYS* 3.3 22.4 + - + +
258A PHE 3.2 7.3 + - - +
259A THR 3.2 0.8 - - - -
260A LYS* 1.3 83.6 - - + +
262A ILE* 1.3 58.6 + - - +
263A LYS 3.6 0.2 - - - -
265A LEU* 3.4 15.6 - - - +
354A LYS* 3.5 17.6 + - - +
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Residues in contact with ILE 262 (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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230A VAL* 3.9 15.3 - - + -
233A PHE* 3.8 15.7 - - + -
258A PHE* 3.2 31.1 + - + +
259A THR 4.0 1.3 - - - +
261A GLU* 1.3 75.9 - - - +
263A LYS* 1.3 67.6 + - - +
264A GLY 3.3 0.3 + - - -
265A LEU* 3.1 28.6 + - + +
281A VAL* 3.6 20.9 - - + +
284A VAL* 3.9 25.4 - - + -
328A LEU* 3.7 28.0 - - + -
346A ILE* 4.2 15.7 - - + -
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Residues in contact with LYS 263 (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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259A THR* 3.0 42.4 + - + +
260A LYS* 4.4 7.9 + - - +
261A GLU 3.6 1.0 - - - -
262A ILE* 1.3 79.4 - - - +
264A GLY* 1.3 61.5 + - - +
265A LEU* 3.2 3.0 + - - +
281A VAL* 3.8 5.6 - - - +
282A CYS* 3.5 31.2 - - - +
283A ASN* 4.5 10.8 + - - +
284A VAL* 6.4 0.2 - - + -
354A LYS* 4.1 17.2 + - - -
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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