Contacts of the helix formed by residues 276 - 284 (chain E) in PDB entry 4QOZ
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 276 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D C 4.1 13.7 - - - +
25D C 5.8 7.2 - - - -
261E ARG* 4.1 9.9 - - - +
274E GLN* 3.1 14.4 + - - +
275E THR* 1.3 75.0 - - - +
277E LEU* 1.3 66.2 + - - +
278E THR* 3.2 34.8 - - + +
279E ILE* 3.1 23.5 + - + +
280E MET* 3.0 25.7 + - - +
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ASP* 5.1 1.1 - - - +
230E ASP* 3.7 19.6 + - - +
261E ARG* 4.6 0.2 - - - +
276E LYS* 1.3 73.9 - - - +
278E THR* 1.3 58.9 + - - +
280E MET* 3.3 11.8 + - + +
281E LEU* 3.0 45.2 + - + +
288E TYR* 3.9 17.0 - - + -
298E ASP* 3.9 40.2 - - + +
301E ASN* 4.3 1.8 - - + -
302E ILE* 3.9 26.9 - - + +
305E ILE* 3.6 23.1 - - + -
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Residues in contact with THR 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E LYS* 3.2 38.8 - - + +
277E LEU* 1.3 80.5 - - - +
279E ILE* 1.3 66.0 + - + +
281E LEU* 3.6 12.6 - - - +
282E GLU* 3.0 25.7 + - - +
288E TYR* 5.8 5.6 - - - +
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Residues in contact with ILE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E PRO 3.6 26.9 - - - +
274E GLN* 4.4 23.1 - - + +
276E LYS* 3.1 33.5 + - + +
278E THR* 1.3 83.2 - - + +
280E MET* 1.3 59.9 + - - +
281E LEU 3.2 0.2 - - - -
282E GLU* 3.1 15.6 + - - +
283E LYS* 2.9 48.0 + - + +
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Residues in contact with MET 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ASP* 3.3 28.7 - - - +
260E ILE* 4.4 17.9 - - + +
261E ARG* 4.3 1.8 - - + -
264E TYR* 2.8 64.9 + - + -
271E PRO 5.9 0.7 - - - -
275E THR* 3.5 30.1 - - + -
276E LYS 3.0 8.2 + - - +
277E LEU* 3.6 23.3 - - + +
279E ILE* 1.3 75.9 - - - +
281E LEU* 1.3 62.9 + - - +
284E LEU* 3.4 12.6 + - - +
302E ILE* 6.0 0.9 - - + -
305E ILE* 3.7 21.8 - - + -
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Residues in contact with LEU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E LEU* 3.0 27.0 + - + +
278E THR* 3.6 11.0 - - - +
280E MET* 1.3 77.0 - - - +
282E GLU* 1.3 61.3 + - - +
284E LEU* 3.2 6.6 + - - -
286E MET* 2.9 59.4 + - + +
288E TYR* 3.6 45.5 - - + +
301E ASN* 4.3 8.3 - - - +
304E ARG* 4.2 13.5 - - - +
305E ILE* 3.7 26.0 - - + -
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Residues in contact with GLU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E VAL* 5.3 1.6 - - - +
278E THR 3.0 18.4 + - - +
279E ILE* 3.1 22.8 + - - +
281E LEU* 1.3 76.7 - - - +
283E LYS* 1.3 66.6 + - + +
285E GLY* 3.0 19.3 + - - -
286E MET 4.4 5.4 - - - -
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Residues in contact with LYS 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLY* 3.2 1.9 - - - -
98E VAL* 3.0 63.3 + - + +
101E VAL* 3.9 4.2 - - + +
264E TYR* 3.4 17.5 - - + +
270E VAL* 4.8 17.7 - - + +
271E PRO* 5.1 12.1 - - - -
279E ILE* 2.9 39.1 + - + +
280E MET* 5.1 0.2 - - - -
282E GLU* 1.3 82.7 + - + +
284E LEU* 1.3 58.5 + - - +
285E GLY 3.2 1.1 - - - -
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Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLU* 5.8 0.9 - - - +
96E ARG* 3.8 18.4 + - - +
97E GLY* 3.9 6.1 - - - -
101E VAL* 3.7 26.5 - - + -
105E ARG* 4.4 2.5 + - - +
264E TYR* 3.4 28.9 - - + +
268E TYR* 3.7 28.5 - - + +
280E MET 3.4 6.4 + - - +
281E LEU 3.2 2.1 + - - +
282E GLU 3.2 0.8 - - - -
283E LYS* 1.3 77.6 - - - +
285E GLY* 1.3 61.7 + - - +
286E MET* 3.3 39.2 + - + +
305E ILE* 4.2 11.9 - - + +
308E ARG* 3.9 20.4 - - + -
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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