Contacts of the strand formed by residues 283 - 294 (chain A) in PDB entry 4N25
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 3.4 1.7 - - - -
274A GLU* 2.8 36.6 + - - +
276A MET* 3.2 30.1 - - - +
281A PRO 4.5 1.2 + - - -
282A LEU* 1.3 71.4 - - - +
284A PRO* 1.3 80.6 - - + +
285A ILE* 3.1 20.1 + - + +
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Residues in contact with PRO 284 (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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203A TYR* 6.0 0.4 - - - +
271A SER* 4.2 4.7 - - - +
272A LEU 3.5 6.1 - - - +
273A LEU* 3.6 16.3 - - + -
282A LEU 3.6 8.0 - - - +
283A THR* 1.3 90.0 - - + +
285A ILE* 1.3 63.4 + - - +
287A THR* 4.1 18.6 - - - +
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Residues in contact with ILE 285 (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 ARG* 3.4 54.2 - - - +
18A VAL 4.7 1.8 - - - +
20A VAL* 5.3 1.6 - - + -
198A TYR* 4.1 11.9 - - + -
272A LEU* 2.7 35.4 + - + +
274A GLU* 3.3 45.3 - - + +
283A THR* 3.7 18.2 - - + +
284A PRO* 1.3 74.6 - - - +
286A PHE* 1.3 58.5 + - + +
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Residues in contact with PHE 286 (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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20A VAL* 3.7 42.6 - - + -
21A LEU 5.0 2.9 - - - -
22A GLY 6.2 0.2 - - - -
23A THR* 4.2 17.5 - - + -
118A ILE* 3.6 46.9 - - + -
270A VAL 5.0 1.1 - - - -
271A SER* 3.1 5.4 + - - -
272A LEU* 2.9 35.0 + - + -
284A PRO 3.5 0.6 - - - -
285A ILE* 1.3 82.3 - - + +
287A THR* 1.3 71.6 + - - +
288A ASP* 3.9 31.0 - - + -
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Residues in contact with THR 287 (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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203A TYR* 3.8 16.0 + - - +
269A HIS* 4.3 5.2 - - + +
270A VAL 3.3 7.9 - - - +
271A SER* 2.6 24.0 + - - +
284A PRO* 4.1 10.7 - - - +
286A PHE* 1.3 86.5 - - - +
288A ASP* 1.3 65.6 + - - +
289A THR* 4.1 16.4 - - - +
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Residues in contact with ASP 288 (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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118A ILE 4.2 0.6 - - - +
119A SER* 3.5 5.8 + - - -
120A LEU* 2.9 18.9 + - - +
133A ASN* 4.9 0.9 - - - +
137A LYS* 2.7 37.9 + - - -
268A ILE 4.1 0.3 - - - +
269A HIS* 3.4 3.8 - - - +
270A VAL* 2.9 47.8 + - + +
286A PHE* 3.9 20.2 - - + -
287A THR* 1.3 74.1 - - - +
289A THR* 1.3 66.6 + - - +
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Residues in contact with THR 289 (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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120A LEU* 5.1 0.2 - - - -
137A LYS* 3.7 11.1 - - - +
138A ALA* 3.7 29.2 - - + +
267A SER* 4.4 8.1 - - - +
268A ILE 3.5 4.3 - - - +
269A HIS* 2.7 39.8 + - + +
287A THR* 4.1 6.9 - - - +
288A ASP* 1.3 79.7 + - - +
290A VAL* 1.3 82.4 + - - +
291A ILE* 5.5 0.7 - - + -
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Residues in contact with VAL 290 (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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120A LEU* 3.1 37.4 - - + +
122A VAL* 3.8 39.7 - - + -
137A LYS* 3.5 11.2 - - + -
138A ALA* 4.6 0.4 - - - +
184A MET* 4.0 19.7 - - - -
267A SER* 3.5 2.9 - - - -
268A ILE* 3.0 44.5 + - + +
289A THR* 1.3 83.2 - - - +
291A ILE* 1.3 60.7 + - - +
292A PHE* 4.2 7.1 - - + -
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Residues in contact with ILE 291 (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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122A VAL* 4.9 0.5 - - - +
137A LYS 3.1 13.0 + - - +
138A ALA 3.6 9.6 - - - +
139A SER* 3.3 35.9 - - - +
140A TRP* 4.0 15.7 - - + +
148A GLY* 5.3 0.2 - - - -
149A ALA* 3.7 19.6 + - - +
265A LEU* 3.9 31.9 - - + -
266A VAL 3.3 14.4 - - - +
267A SER* 4.3 9.6 - - - +
289A THR* 5.6 0.9 - - + -
290A VAL* 1.3 76.2 - - - +
292A PHE* 1.3 75.1 + - - +
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Residues in contact with PHE 292 (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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122A VAL* 3.5 26.7 - - + -
123A ASP 5.9 0.2 - - - -
140A TRP* 4.3 1.1 - - - -
149A ALA* 3.3 33.7 - - + -
150A ILE 4.0 9.6 - - - -
151A LEU* 4.0 16.8 - - + -
182A SER* 3.9 20.0 - - - -
183A GLN 4.6 3.6 - - - -
184A MET* 4.4 4.0 - - + -
252A VAL* 4.1 24.5 - - + -
264A GLY 3.7 0.3 - - - +
265A LEU* 3.4 10.1 - - - +
266A VAL* 2.8 50.2 + - + +
268A ILE* 3.9 29.4 - - + -
290A VAL* 4.2 7.6 - - + -
291A ILE* 1.3 75.9 - - - +
293A ARG* 1.3 60.0 + - - +
294A ILE 4.1 0.4 - - - -
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Residues in contact with ARG 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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140A TRP* 3.3 54.3 + - + +
142A TRP* 3.8 27.0 - - - +
149A ALA 2.9 8.1 + - - -
150A ILE* 3.4 6.8 - - - +
151A LEU* 2.9 21.7 + - - -
258A PRO* 5.4 2.4 - - - +
263A SER* 3.0 29.5 + - - -
264A GLY* 3.4 6.3 - - - +
265A LEU* 3.6 31.1 - - + +
292A PHE* 1.3 75.4 - - - +
294A ILE* 1.3 76.0 + - - +
295A ALA 3.5 0.9 + - - -
296A PRO* 5.6 0.4 - - - -
455A GLN* 3.9 13.7 - - - +
660A TRP* 3.7 17.0 - - + -
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Residues in contact with ILE 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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151A LEU* 3.3 31.4 - - + +
153A VAL* 3.4 33.0 - - + +
211A LYS 3.7 23.1 - - - +
254A GLY* 4.1 6.3 - - - -
256A CYS 3.5 19.7 - - - +
258A PRO* 4.0 17.5 - - + +
262A PHE* 3.8 21.1 - - + -
264A GLY* 2.9 17.9 + - - +
266A VAL* 4.3 8.1 - - + -
293A ARG* 1.3 83.6 - - - +
295A ALA* 1.3 69.0 + - - +
296A PRO* 3.6 2.9 - - - +
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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