Contacts of the strand formed by residues 376 - 383 (chain A) in PDB entry 1SEK
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 ASN 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN* 5.0 3.2 + - - -
19A LEU* 4.6 14.5 - - - +
20A ARG* 3.3 35.8 - - - +
23A ASN* 4.0 13.5 + - - +
24A ASP* 4.9 2.0 - - - +
48A PHE* 4.1 15.4 - - + -
88A LEU* 6.0 0.6 - - - +
372A LYS* 4.1 3.1 - - - -
373A TYR 2.6 44.7 + - - +
374A ASN* 3.1 24.0 + - - +
375A ARG* 1.3 74.5 - - - +
377A SER* 1.3 63.2 + - - +
378A MET* 3.2 18.9 + - + +
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Residues in contact with SER 377 (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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23A ASN* 3.3 22.7 + - - +
24A ASP* 5.0 6.0 + - - -
27A THR* 4.5 21.2 + - - +
47A ALA 5.7 0.3 + - - -
48A PHE* 3.8 6.9 + - - +
265A LEU* 4.6 8.0 - - - +
370A SER* 3.6 19.8 + - - -
371A LEU 3.1 6.7 - - - -
372A LYS* 3.0 23.0 - - - +
376A ASN* 1.3 69.1 - - - +
378A MET* 1.3 66.1 + - - +
379A PHE* 3.3 4.3 + - - -
380A SER* 5.5 0.4 - - - -
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Residues in contact with MET 378 (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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46A SER* 2.5 30.4 + - - -
48A PHE* 3.7 41.4 + - + +
100A LEU* 3.7 26.0 - - + -
102A MET* 3.5 11.6 - - + +
371A LEU* 2.7 30.6 + - + +
373A TYR* 3.6 36.8 - - + +
376A ASN* 3.3 39.3 - - + +
377A SER* 1.3 73.6 - - - +
379A PHE* 1.3 56.8 + - + +
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Residues in contact with PHE 379 (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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27A THR* 6.0 1.3 - - - -
44A VAL* 3.8 14.8 - - + -
45A LEU 3.0 19.3 - - - +
46A SER* 3.9 9.4 - - - +
100A LEU* 4.8 0.9 - - + -
178A ILE* 4.0 17.5 - - + -
180A PHE* 3.6 31.9 - + + -
241A MET* 4.8 6.3 - - + -
333A ILE* 3.4 28.0 - - + -
369A PHE* 3.7 22.9 - + - -
370A SER* 3.2 6.3 + - - -
371A LEU* 3.0 65.1 + - + -
377A SER* 3.3 4.4 - - - -
378A MET* 1.3 82.5 - - + +
380A SER* 1.3 61.9 + - - +
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Residues in contact with SER 380 (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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27A THR* 4.0 21.8 - - - +
31A PHE* 3.7 15.1 - - - -
44A VAL* 3.5 1.6 - - - +
45A LEU* 2.8 40.9 + - - +
368A PHE* 4.0 14.8 - - - -
369A PHE* 3.4 19.5 - - - -
370A SER* 4.0 9.4 - - - +
377A SER* 5.5 0.7 - - - -
379A PHE* 1.3 78.4 - - - +
381A GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 381 (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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31A PHE* 4.1 10.4 - - - -
43A VAL* 3.1 14.1 - - - -
45A LEU* 4.7 2.0 - - - -
368A PHE* 3.4 9.4 - - - -
369A PHE* 3.0 39.2 + - - -
380A SER* 1.3 80.0 - - - +
382A VAL* 1.3 64.5 + - - -
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Residues in contact with VAL 382 (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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31A PHE* 3.8 21.8 - - + -
35A VAL* 4.3 4.5 - - + -
41A GLN 3.8 7.2 - - - +
42A ASN* 3.5 2.6 - - - -
43A VAL* 3.0 53.2 + - + +
252A ILE* 4.3 18.4 - - + -
256A GLU* 3.7 24.7 - - + +
286A ILE* 3.8 3.5 - - - +
367A PHE 3.4 7.0 - - - +
368A PHE* 4.4 5.2 - - + -
369A PHE* 3.8 3.6 - - - -
381A GLY* 1.3 79.7 - - - +
383A CYS* 1.3 59.7 + - - +
384A VAL* 4.5 8.5 - - + -
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Residues in contact with CYS 383 (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 ASN* 3.6 9.6 - - - -
198A PHE* 4.5 0.7 - - - -
284A PHE* 4.2 17.9 - - + -
286A ILE* 4.2 11.7 - - + -
366A PRO* 3.3 2.8 - - - +
367A PHE* 2.9 64.9 + - + -
369A PHE* 4.3 2.7 - - + -
382A VAL* 1.3 74.0 - - - +
384A VAL* 1.3 61.2 + - - +
385A GLN 4.6 0.2 - - - -
386A PRO* 3.9 35.2 - - - -
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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