Contacts of the strand formed by residues 253 - 264 (chain 1) in PDB entry 1AR9
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 VAL 253 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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931 ASP* 3.3 4.9 - - - +
941 ASN* 3.0 33.8 + - + +
1401 ALA* 3.8 17.0 - - + -
1411 ASN 3.5 11.4 - - - +
1421 PHE* 3.7 28.3 - - + -
1501 ALA* 3.8 20.6 - - + -
1531 GLN* 3.5 34.5 + - - +
2511 THR 3.6 2.9 + - - +
2521 LYS* 1.3 79.5 - - - +
2541 THR* 1.3 66.6 + - - +
2551 SER* 5.0 0.2 + - - -
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Residues in contact with THR 254 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911 THR* 3.9 19.5 - - + -
921 VAL 3.6 12.1 - - - +
931 ASP* 4.0 3.1 - - + +
1401 ALA* 3.4 0.7 - - - -
1411 ASN* 2.9 45.9 + - - +
1431 THR* 3.7 24.1 + - - +
2521 LYS* 3.8 16.5 + - - -
2531 VAL* 1.3 76.7 - - - +
2551 SER* 1.3 66.8 + - - +
2561 LYS* 5.4 4.9 - - + -
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Residues in contact with SER 255 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911 THR* 3.5 2.3 - - - +
921 VAL* 2.8 41.5 + - - +
1381 VAL* 4.8 0.7 - - - -
1391 THR 3.3 11.4 - - - -
1401 ALA* 3.4 9.9 - - - +
1411 ASN* 5.4 0.2 - - - -
1531 GLN* 3.6 8.3 + - - -
1551 TYR* 2.7 42.7 + - - -
2441 VAL* 4.7 1.2 - - - +
2531 VAL* 4.2 2.0 + - - +
2541 THR* 1.3 74.1 - - - +
2561 LYS* 1.3 71.1 + - - +
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Residues in contact with LYS 256 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891 ILE* 4.0 20.2 - - + +
901 MET 3.3 9.2 - - - +
911 THR* 3.6 24.5 - - + +
1371 VAL 3.5 1.7 - - - +
1381 VAL* 3.4 5.1 - - - +
1391 THR* 2.8 39.9 + - - +
2541 THR* 5.4 4.5 - - + -
2551 SER* 1.3 79.1 - - - +
2571 ILE* 1.3 63.5 + - - +
2581 ARG* 3.9 26.1 + - - +
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Residues in contact with ILE 257 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881 THR 3.9 0.2 - - - +
891 ILE* 3.5 1.6 - - - -
901 MET* 2.8 51.5 + - + +
921 VAL* 3.7 25.4 - - + -
1361 PHE* 4.0 35.0 - - + -
1371 VAL 3.5 2.2 - - - -
1381 VAL* 4.0 19.1 - - + -
1551 TYR* 4.3 11.7 - - + -
1571 ILE* 4.5 8.3 - - + -
2421 VAL* 3.7 33.7 - - + -
2561 LYS* 1.3 76.8 - - - +
2581 ARG* 1.3 62.6 + - - +
2591 VAL* 3.7 7.3 + - + +
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Residues in contact with ARG 258 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 CYS* 4.7 4.2 - - - -
881 THR 3.6 3.4 - - - +
891 ILE* 3.7 39.1 - - + +
1351 THR 3.6 1.4 - - - +
1361 PHE* 3.4 6.4 - - - -
1371 VAL* 2.8 49.8 + - + +
1391 THR* 3.8 22.8 + - - +
2561 LYS* 3.9 24.0 + - - +
2571 ILE* 1.3 73.3 - - - +
2591 VAL* 1.3 60.8 + - - +
2601 TYR* 3.4 32.3 - - + +
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Residues in contact with VAL 259 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 CYS* 3.3 4.0 - - - -
871 VAL* 2.8 42.4 + - + +
881 THR* 3.0 34.9 + - + -
901 MET* 4.5 4.0 - - - -
1081 TRP* 4.4 8.7 - - + -
1341 LEU* 4.1 21.5 - - + -
1351 THR 3.7 2.9 - - - +
1361 PHE* 3.8 31.0 - - + -
2401 LEU* 4.5 10.1 - - + -
2571 ILE* 4.3 10.5 - - + +
2581 ARG* 1.3 75.2 - - - +
2601 TYR* 1.3 63.9 + - - +
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Residues in contact with TYR 260 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841 GLY* 4.3 9.6 - - - -
851 ALA 3.2 7.0 - - - +
861 CYS* 3.5 35.1 - - + +
1331 GLU 3.3 1.4 - - - +
1341 LEU* 3.2 9.4 - - - +
1351 THR* 2.8 49.2 + - - +
1371 VAL* 3.6 23.0 - - + +
2581 ARG* 3.4 45.1 - - + -
2591 VAL* 1.3 72.9 - - - +
2611 LEU* 1.3 60.0 + - - +
2621 LYS 4.1 0.2 + - - -
133 TYR* 3.3 37.7 - + - +
153 THR* 4.9 7.0 - - + -
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Residues in contact with LEU 261 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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01 SPH 5.7 2.5 - - + -
831 ARG 3.6 2.3 - - - +
841 GLY* 3.5 0.6 - - - -
851 ALA* 2.9 31.4 + - - +
871 VAL* 3.9 31.9 - - + -
1081 TRP* 6.1 1.3 - - + -
1101 ILE* 6.1 2.5 - - + -
1111 THR 5.0 2.9 - - - +
1121 TYR* 4.5 15.7 - - + +
1181 LEU* 4.0 13.3 - - + +
1221 LEU* 6.0 0.4 - - + -
1301 PHE* 4.5 9.6 - - + -
1321 MET* 3.6 44.4 - - + -
1331 GLU 3.6 2.5 - - - -
1341 LEU* 4.0 6.1 - - + -
2591 VAL 4.1 0.8 + - - -
2601 TYR* 1.3 73.6 - - - +
2621 LYS* 1.3 62.5 + - - +
2631 PRO* 3.7 23.7 - - + +
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Residues in contact with LYS 262 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811 PHE 4.1 2.9 - - - +
821 ALA* 3.9 11.7 - - + +
831 ARG* 3.6 36.1 - - - +
841 GLY* 4.0 7.2 - - - +
1311 ASP 3.7 0.2 - - - +
1321 MET* 3.7 0.9 - - - -
1331 GLU* 2.9 75.3 + - + +
2601 TYR 4.2 0.2 - - - -
2611 LEU* 1.3 76.5 - - - +
2631 PRO* 1.3 71.9 - - + +
2641 LYS* 3.3 18.9 + - + +
153 THR 4.8 2.2 - - - +
173 ASP* 3.0 29.7 + - - +
183 ASN* 4.0 15.0 + - - +
193 PHE 4.9 1.0 + - - +
414 ALA* 6.0 1.0 - - - +
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Residues in contact with PRO 263 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781 GLU* 4.5 2.3 - - - +
811 PHE* 4.1 41.3 - - + +
821 ALA* 5.2 1.4 + - - -
831 ARG 4.5 1.3 - - - +
1181 LEU* 4.5 13.0 - - + -
1221 LEU* 4.7 5.6 - - + -
1301 PHE* 3.6 29.4 - - + -
1311 ASP 3.6 6.1 - - - +
2611 LEU* 3.7 18.6 - - + +
2621 LYS* 1.3 87.6 - - - +
2641 LYS* 1.3 60.0 + - - +
2661 ILE* 3.9 23.4 - - + +
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Residues in contact with LYS 264 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781 GLU* 3.7 6.3 - - - +
1301 PHE* 3.4 1.9 - - - +
1311 ASP* 2.8 43.5 + - + +
1321 MET 5.2 0.2 - - - -
1331 GLU* 4.0 27.4 - - + -
1951 SER* 2.9 18.9 + - - -
2621 LYS* 3.3 22.8 + - - +
2631 PRO* 1.3 72.5 - - - +
2651 HIS* 1.3 87.5 + - + +
2661 ILE 3.3 1.1 + - - -
183 ASN* 6.1 0.2 - - - +
193 PHE 4.7 5.7 + - - -
213 SER* 4.7 0.6 + - - -
374 ALA 2.5 28.6 + - - +
384 SER 3.5 7.3 + - - -
394 ASN 3.0 18.6 + - - +
404 ALA* 5.1 1.1 - - - +
414 ALA* 5.0 7.0 - - + +
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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