Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 1ADI
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 TYR 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY* 4.7 2.2 - - - -
3A ASN 3.1 4.1 + - - +
4A VAL* 3.3 13.5 - - + -
5A VAL* 2.9 25.3 + - - +
259A VAL* 3.8 2.2 - - - +
260A ASP* 1.3 83.2 - - + +
262A VAL* 1.3 68.0 + - - +
263A LEU* 3.9 24.3 - - + +
325A SER* 3.9 17.5 - - - -
326A GLY* 3.4 13.0 - - - -
411A ASP* 2.5 30.0 + - - +
426A ARG* 3.9 14.4 - - - -
428A PRO* 3.6 51.5 - - + +
431A ALA* 3.8 24.7 - - + +
257B ARG* 5.0 0.2 - - - +
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Residues in contact with VAL 262 (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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5A VAL* 3.5 7.6 - - + +
7A LEU* 3.6 19.3 - - + -
245A ALA* 4.4 11.7 - - + -
259A VAL* 4.1 21.1 - - + -
261A TYR* 1.3 76.7 - - - +
263A LEU* 1.3 58.7 + - - +
264A GLY 3.6 2.9 + - - -
322A ASN* 3.4 28.9 - - + +
323A SER* 3.9 13.7 - - - +
324A LEU* 3.5 20.5 - - + -
325A SER* 3.2 25.6 + - - -
326A GLY 3.7 4.5 + - - -
256B PRO* 5.1 0.7 - - + -
257B ARG* 4.1 8.1 - - + -
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Residues in contact with LEU 263 (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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4A VAL* 4.9 2.2 - - + -
5A VAL 2.8 14.9 + - - +
6A VAL* 4.3 7.4 - - + -
7A LEU* 3.0 28.7 + - - +
19A ILE* 3.7 30.7 - - + -
23A LEU* 4.0 14.4 - - + -
261A TYR* 3.9 18.8 - - + +
262A VAL* 1.3 68.4 - - - +
264A GLY* 1.3 59.4 + - - +
265A ILE* 3.5 14.8 + - + +
326A GLY 3.7 13.5 - - - +
327A PHE 4.3 6.3 - - - +
328A CYS* 3.9 22.2 - - + -
411A ASP* 5.5 0.2 - - + -
412A ILE* 4.3 10.5 - - + -
428A PRO* 4.1 19.3 - - + -
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Residues in contact with GLY 264 (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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7A LEU 3.2 6.5 - - - -
9A THR* 3.4 21.1 - - - -
262A VAL 3.6 2.8 + - - -
263A LEU* 1.3 71.9 - - - +
265A ILE* 1.3 64.8 + - - -
266A LEU 3.2 3.6 + - - -
324A LEU* 3.6 11.3 - - - +
326A GLY 3.0 13.6 + - - -
327A PHE* 3.3 19.2 - - - -
328A CYS 3.4 9.4 + - - -
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Residues in contact with ILE 265 (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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6A VAL* 3.9 23.6 - - + -
7A LEU 2.6 26.5 + - - +
8A GLY* 3.9 7.0 - - - -
9A THR* 3.0 23.1 + - - -
14A GLU* 3.5 26.7 - - + +
15A GLY 3.7 21.5 - - - +
16A LYS* 3.9 17.0 - - + -
19A ILE* 4.0 22.0 - - + -
263A LEU* 3.9 18.4 - - + +
264A GLY* 1.3 67.4 - - - -
266A LEU* 1.3 62.6 + - - +
328A CYS* 4.0 5.6 - - + +
330A THR* 4.1 9.2 - - + -
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Residues in contact with LEU 266 (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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9A THR* 3.4 16.2 - - - +
10A GLN* 3.9 12.1 - - - +
14A GLU* 4.8 0.4 - - - -
264A GLY 3.2 1.8 + - - +
265A ILE* 1.3 74.7 - - - +
267A LYS* 1.3 57.9 + - - +
310A LEU* 4.3 12.8 - - + -
315A VAL* 3.9 28.7 - - + -
327A PHE* 3.9 31.4 - - + -
328A CYS 3.2 9.0 + - - +
329A LEU* 3.2 19.7 - - + +
330A THR* 2.6 37.2 + - - -
402A ILE* 3.9 28.5 - - + -
410A ILE* 4.8 1.1 - - + -
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Residues in contact with LYS 267 (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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10A GLN* 2.9 28.4 + - - +
12A GLY 5.2 1.8 - - - -
13A ASP* 3.2 31.2 + - - +
14A GLU* 4.0 11.5 - - - +
265A ILE 4.2 0.4 + - - -
266A LEU* 1.3 71.7 - - - +
268A ALA* 1.3 56.1 + - - +
269A TYR* 2.7 53.1 + - + +
270A SER* 5.0 0.2 - - - +
271A THR* 3.0 47.8 + - - +
296A GLU* 3.3 16.7 + - - +
310A LEU* 3.5 6.1 - - - +
329A LEU* 4.2 1.1 - - - -
330A THR* 3.0 18.6 - - - +
331A LYS* 4.6 9.6 - - + -
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Residues in contact with ALA 268 (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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267A LYS* 1.3 68.8 - - - +
269A TYR* 1.3 58.3 + - + +
309A TRP* 6.2 0.2 - - - -
310A LEU* 4.2 10.1 + - - +
329A LEU* 3.6 19.9 - - + +
330A THR 2.7 22.1 + - - +
331A LYS 3.8 5.2 - - - +
332A LEU* 3.7 26.5 - - + -
335A LEU* 3.7 12.8 - - + +
398A TYR* 2.7 33.4 + - + -
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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