Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 1EG2
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLY 4.7 5.8 - - - +
37A THR* 1.3 77.6 + - - +
39A ARG* 1.3 64.7 + - - +
40A HIS* 2.9 25.3 + - - -
243A GLY* 5.3 2.7 - - - -
261A ILE* 4.7 5.7 + - - -
264A GLY* 3.5 28.5 - - - +
265A ARG 3.4 16.8 + - - +
266A ASN* 3.2 11.4 - - - +
298A SER 3.0 7.0 + - - +
299A TYR* 3.1 14.4 - - - +
300A GLU* 2.8 26.0 + - - +
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Residues in contact with ARG 39 (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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37A THR* 4.2 7.7 + - - +
38A THR* 1.3 77.0 - - - +
40A HIS* 1.3 64.0 + - - +
41A VAL* 5.6 0.2 - - + -
266A ASN* 2.8 16.0 + - - +
267A SER 3.1 20.6 + - - -
300A GLU* 3.5 32.5 - - + +
302A VAL* 5.5 2.0 - - + -
310A ALA* 2.6 53.3 + - + +
311A ALA* 3.7 4.8 - - - +
313A GLN* 2.6 58.0 + - - +
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Residues in contact with HIS 40 (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 THR* 2.9 28.2 + - - -
39A ARG* 1.3 77.8 - - - +
41A VAL* 1.3 59.4 + - - +
257A ALA 4.3 0.8 + - - -
260A ALA* 3.8 2.2 - - + +
261A ILE* 3.2 43.2 - - + +
265A ARG 2.9 25.1 + - - -
267A SER* 2.7 32.1 + - - +
280A TYR* 3.5 19.1 - - - +
299A TYR* 4.0 5.2 - - + -
300A GLU 2.9 14.8 + - - -
301A ILE* 3.4 12.5 - - + +
302A VAL* 2.7 32.8 + - - +
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Residues in contact with VAL 41 (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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40A HIS* 1.3 79.7 - - - +
42A TYR* 1.3 66.6 + - - +
267A SER* 2.9 8.0 + - - +
268A ILE* 3.3 6.1 - - + +
269A CYS* 2.9 24.6 + - - +
280A TYR* 4.5 2.5 + - - -
302A VAL* 3.1 16.8 - - + +
304A GLY 3.2 28.9 - - - +
307A ASN* 3.3 22.9 - - + +
308A PHE* 3.8 22.4 - - + -
310A ALA* 4.1 8.5 - - + -
311A ALA* 3.9 20.9 - - + +
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Residues in contact with TYR 42 (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 VAL* 1.3 78.2 - - - +
43A ASP* 1.3 68.8 + - - +
269A CYS 3.0 14.6 - - - +
270A THR* 4.7 1.6 - - - -
276A PHE* 4.1 8.7 - + + -
277A LYS* 3.6 37.0 - - + +
280A TYR* 3.5 52.3 - + + -
281A GLN* 4.5 9.5 + - + +
284A LEU* 6.0 0.2 - - + -
301A ILE* 3.8 20.4 - - + -
302A VAL 3.2 7.5 + - - -
303A GLU* 3.5 45.9 + - + +
304A GLY* 2.9 24.6 + - - -
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Residues in contact with ASP 43 (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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42A TYR* 1.3 85.6 - - - +
44A VAL* 1.3 83.7 + - - +
45A CYS* 4.0 3.0 - - - +
269A CYS 3.3 3.4 + - - -
270A THR* 3.2 34.5 - - + +
271A ASP 3.4 2.9 + - - -
276A PHE* 3.4 6.6 - - - -
303A GLU* 4.8 8.6 - - - +
304A GLY* 3.6 9.7 + - - -
305A ALA* 2.9 38.9 + - + +
308A PHE* 5.1 0.2 - - + -
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Residues in contact with VAL 44 (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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42A TYR* 6.1 0.4 - - + -
43A ASP* 1.3 89.7 + - - +
45A CYS* 1.3 66.8 - - - +
271A ASP 3.1 13.2 - - - +
272A ALA 3.6 17.9 - - - +
273A ALA 3.8 13.5 - - - +
274A PRO* 3.8 33.2 - - + +
276A PHE* 4.3 9.6 - - + -
277A LYS* 4.4 11.2 - - + +
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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