Contacts of the strand formed by residues 326 - 335 (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 ALA 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ALA* 5.2 11.7 - - + +
166A LEU* 6.0 0.4 - - + -
172A SER 3.6 2.2 + - - -
173A VAL* 3.2 22.3 - - + -
174A LEU 2.8 24.7 + - - +
293A LYS* 5.0 6.5 - - - -
305A PHE* 5.6 0.2 - - - -
324A VAL* 3.5 6.3 - - - +
325A ASP* 1.3 82.9 - - + +
327A ALA* 1.3 61.2 + - - +
328A ILE* 5.0 11.9 - - + -
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Residues in contact with ALA 327 (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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174A LEU* 3.1 23.1 - - + +
291A ASP* 3.7 4.5 + - - +
292A LEU* 3.0 42.5 + - + -
293A LYS* 3.6 14.3 + - - +
296A LEU* 5.3 0.7 - - + -
305A PHE* 4.1 19.7 - - + -
324A VAL* 4.7 0.2 - - + -
326A ALA* 1.3 75.3 - - - +
328A ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.0 32.6 - - + +
161A VAL* 4.4 21.3 - - + -
162A ASP 5.3 0.4 - - - +
165A ALA* 5.2 11.7 - - + -
173A VAL* 5.8 3.1 - - + -
174A LEU 2.8 11.8 + - - +
175A VAL* 3.3 4.3 - - + +
176A ASN* 2.6 33.6 + - - +
289A THR* 3.9 28.0 - - + -
290A THR 3.7 5.6 - - - +
291A ASP* 5.5 3.6 - - - +
292A LEU* 3.9 4.4 - - - +
326A ALA* 5.0 10.3 - - + -
327A ALA* 1.3 83.6 - - - +
329A GLN* 1.3 60.2 + - - +
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Residues in contact with GLN 329 (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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30A MET* 4.0 10.5 - - - +
44A VAL 4.9 0.2 - - - +
45A LEU* 3.8 9.5 - - - +
46A SER 2.9 44.4 + - - +
49A SER* 3.4 2.4 + - - -
50A VAL* 3.2 9.1 - - - +
176A ASN* 2.6 37.1 - - - +
178A ILE* 4.5 6.7 - - + -
288A THR 3.8 0.5 - - - +
289A THR* 3.5 1.9 - - - -
290A THR* 2.7 47.5 + - - +
292A LEU* 3.6 21.5 - - + +
328A ILE* 1.3 75.5 - - - +
330A LYS* 1.3 69.6 + - - +
331A ALA* 4.6 3.7 - - + +
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Residues in contact with LYS 330 (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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157A ILE* 3.7 25.7 - - + +
158A LYS 3.1 20.0 + - - +
159A ASN* 4.1 8.2 + - - +
160A LEU* 3.4 36.1 - - + +
176A ASN 2.7 8.7 + - - -
177A ALA* 3.3 4.0 - - - +
178A ILE* 3.0 24.1 + - - +
287A GLU* 3.8 36.8 + - - +
288A THR 3.4 4.0 - - - +
289A THR* 3.5 26.5 - - + +
329A GLN* 1.3 75.0 - - - +
331A ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 331 (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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44A VAL* 3.7 33.8 - - + +
45A LEU* 4.9 2.0 - - - -
178A ILE* 3.4 24.7 - - + +
286A ILE 3.6 1.0 - - - +
287A GLU* 3.1 5.5 - - - +
288A THR 2.8 40.0 + - - +
329A GLN* 4.2 8.5 - - - +
330A LYS* 1.3 74.7 - - - +
332A PHE* 1.3 61.1 + - - +
333A ILE* 4.8 2.5 - - + -
379A PHE* 6.5 0.2 - - + -
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Residues in contact with PHE 332 (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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156A ARG* 3.8 23.8 - - + -
157A ILE* 3.9 14.5 - - + +
178A ILE 3.1 6.9 + - - -
179A TYR* 3.4 26.5 - + + -
180A PHE 3.1 24.1 + - - -
285A LYS* 3.9 23.8 - - + -
286A ILE 3.3 10.1 - - - -
287A GLU* 3.7 32.3 - - + +
331A ALA* 1.3 74.3 - - - +
333A ILE* 1.3 77.3 + - - +
334A GLU* 3.8 26.5 - - - -
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Residues in contact with ILE 333 (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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44A VAL* 3.3 30.5 - - + -
178A ILE* 4.9 5.6 - - + -
180A PHE* 3.7 9.9 - - + +
241A MET* 6.0 0.7 - - + -
284A PHE* 4.3 22.4 - - + -
285A LYS* 3.0 8.7 - - - +
286A ILE* 2.7 45.3 + - + +
331A ALA* 4.8 3.6 - - + -
332A PHE* 1.3 86.6 - - - +
334A GLU* 1.3 63.5 + - - +
335A VAL* 4.3 8.3 - - + -
369A PHE* 4.7 7.4 - - + -
379A PHE* 3.4 45.3 - - + -
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Residues in contact with GLU 334 (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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156A ARG* 5.7 0.2 - - - +
179A TYR* 3.8 15.4 + - + +
180A PHE* 2.9 27.8 + - - +
181A LYS* 3.8 43.3 + - + +
182A GLY 4.4 1.6 + - - -
284A PHE 3.9 1.3 - - - -
285A LYS* 2.9 39.1 + - + +
332A PHE* 3.8 18.7 - - + -
333A ILE* 1.3 74.3 - - - +
335A VAL* 1.3 69.9 + - - +
336A ASN* 4.2 7.0 + - + +
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Residues in contact with VAL 335 (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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180A PHE* 5.0 2.9 - - + -
184A TRP* 4.3 18.2 - - + -
211A MET* 4.3 17.5 - - + -
234A TYR* 4.8 4.5 - - - +
241A MET* 4.0 20.9 - - + -
281A LEU* 4.6 3.6 - - + -
283A LYS* 3.5 5.0 - - - +
284A PHE* 2.8 76.3 + - + +
333A ILE* 4.3 6.7 - - + -
334A GLU* 1.3 80.1 - - - +
336A ASN* 1.3 64.3 + - - +
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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