Contacts of the helix formed by residues 292 - 299 (chain A) in PDB entry 1EXD
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 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.3 3.6 - - + -
39A LEU 3.2 15.9 - - - +
40A HIS* 3.6 2.7 - - - +
273A LEU* 4.6 11.2 - - + -
285A TRP* 2.6 55.8 + - + +
290A MET* 3.1 12.4 - - + +
291A PRO* 1.3 81.1 - - - +
293A ILE* 1.3 61.1 + - - +
294A SER* 3.9 5.4 - - - -
295A GLY* 2.9 20.9 + - - -
296A LEU* 3.0 26.4 + - - +
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Residues in contact with ILE 293 (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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39A LEU* 2.8 36.4 + - + +
40A HIS 3.6 22.0 - - - +
41A ILE* 4.0 3.4 - - - +
44A ALA* 3.8 22.9 - - + +
47A ILE* 5.7 0.2 - - + -
84A ASP* 3.6 26.0 - - + +
87A TRP* 3.6 35.1 - - + -
88A LEU* 4.5 10.8 - - + -
292A THR* 1.3 69.5 - - - +
294A SER* 1.3 56.1 + - - +
296A LEU* 3.3 5.4 + - + +
297A ARG* 2.8 35.5 + - - +
306A ILE* 4.7 10.5 - - + -
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Residues in contact with SER 294 (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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38A TYR* 3.8 23.9 - - - +
39A LEU 4.7 0.2 + - - -
84A ASP* 3.6 7.9 + - - -
285A TRP 3.9 0.3 + - - -
286A ASP* 3.8 22.8 - - - +
292A THR* 3.7 8.1 + - - -
293A ILE* 1.3 77.5 - - - +
295A GLY* 1.3 58.9 + - - +
297A ARG* 3.5 32.3 + - - +
298A ARG* 2.9 30.7 + - - +
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Residues in contact with GLY 295 (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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286A ASP 3.5 16.4 - - - -
287A ASP 3.6 10.3 - - - -
288A PRO* 3.9 3.0 - - - +
290A MET 4.2 6.3 - - - -
292A THR* 2.9 22.7 + - - -
294A SER* 1.3 76.2 + - - +
296A LEU* 1.3 58.7 + - - +
297A ARG 3.1 0.2 + - - -
298A ARG* 3.2 2.9 + - - +
299A ARG* 2.8 31.7 + - - +
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Residues in contact with LEU 296 (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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41A ILE* 3.9 31.4 - - + -
87A TRP* 5.3 0.2 - - - -
288A PRO 5.6 1.1 - - - +
290A MET 4.1 9.8 + - - +
291A PRO* 4.0 13.5 - - + +
292A THR 3.0 23.2 + - - +
293A ILE* 3.8 5.6 - - + +
295A GLY* 1.3 74.4 - - - +
297A ARG* 1.3 54.1 + - - +
299A ARG* 3.4 8.3 + - + +
300A GLY 3.1 4.5 + - - -
301A TYR* 2.7 67.8 + - + +
306A ILE* 4.0 16.6 - - + -
327A LEU* 4.3 17.7 - - + -
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Residues in contact with ARG 297 (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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83A ASN* 3.6 22.9 + - - +
84A ASP* 2.8 30.7 + - - +
87A TRP* 3.2 68.6 - - + +
293A ILE 2.8 17.8 + - - +
294A SER* 3.5 22.1 + - - +
295A GLY 3.1 0.2 - - - -
296A LEU* 1.3 74.5 - - - +
298A ARG* 1.3 58.7 + - - +
300A GLY* 2.6 27.2 + - - -
301A TYR 3.8 10.4 + - - +
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Residues in contact with ARG 298 (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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283A GLU* 2.9 37.8 + - - +
286A ASP* 3.0 46.3 + - + +
287A ASP* 4.2 2.4 - - - +
288A PRO* 3.5 20.6 - - + +
294A SER 2.9 21.2 + - - +
295A GLY 3.8 0.2 - - - +
297A ARG* 1.3 74.6 - - - +
299A ARG* 1.3 59.8 + - - +
300A GLY 3.3 0.5 + - - -
470A ARG* 4.8 1.2 - - - +
472A TYR* 4.9 0.2 + - - -
525A CYS* 3.9 6.2 - - - -
526A LEU 4.9 0.2 - - - +
527A ASP* 4.4 14.5 - - - +
528A SER* 2.6 51.3 + - - +
529A ARG* 3.8 14.8 - - - +
530A HIS* 3.6 2.2 + - - -
539A ASN* 3.0 21.1 + - - -
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Residues in contact with ARG 299 (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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288A PRO* 3.1 43.2 + - + +
289A ARG* 4.2 7.3 - - - +
295A GLY 2.8 16.9 + - - +
296A LEU* 3.6 9.2 - - + +
297A ARG 3.1 0.2 - - - -
298A ARG* 1.3 77.0 - - - +
300A GLY* 1.3 58.0 + - - +
301A TYR* 4.0 24.2 + - + -
328A GLU* 5.3 6.5 + - - -
472A TYR* 3.2 41.9 + - - +
473A ASP* 4.6 8.9 + - - +
525A CYS* 3.8 5.9 - - - -
539A ASN* 4.4 4.0 - - - +
540A ARG 3.5 9.6 + - - -
541A THR* 2.7 45.1 + - - +
542A VAL* 5.4 1.2 - - - +
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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