Contacts of the strand formed by residues 254 - 272 (chain 1) in PDB entry 3EPD
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 254 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931 ASP* 3.6 2.6 - - - +
941 ASN* 2.9 33.7 + - - +
1401 ALA* 4.1 19.5 - - + -
1411 ASN 3.7 13.0 - - - +
1421 PHE* 4.2 12.8 - - + -
1501 ALA* 3.7 29.6 - - + -
1531 GLN* 3.5 33.4 - - - +
2501 ASN* 4.9 1.8 - - - +
2521 THR 4.2 6.3 - - - +
2531 LYS* 1.3 79.5 - - - +
2551 THR* 1.3 62.1 + - - +
2561 SER* 4.4 1.8 + - - +
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Residues in contact with THR 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 GLU* 3.5 30.1 - - + +
921 VAL 3.9 0.2 - - - -
931 ASP* 3.1 23.2 + - - +
1401 ALA* 3.2 2.9 - - - +
1411 ASN* 3.0 44.5 + - - +
1431 THR* 3.2 26.0 - - - +
2531 LYS* 3.8 7.0 - - - -
2541 VAL* 1.3 71.5 - - - +
2561 SER* 1.3 66.8 + - - +
2571 LYS* 5.5 3.8 - - + -
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Residues in contact with SER 256 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 ILE 4.4 0.2 - - - -
911 GLU* 3.4 7.3 - - - +
921 VAL* 2.9 39.2 + - - -
1381 VAL* 4.8 0.7 - - - -
1391 THR 3.2 11.2 - - - -
1401 ALA* 3.6 5.5 - - - +
1531 GLN* 3.8 7.3 + - - -
1551 TYR* 2.7 44.7 + - - -
2451 VAL* 4.8 1.4 - - - +
2541 VAL* 4.4 1.0 + - - +
2551 THR* 1.3 78.6 + - - +
2571 LYS* 1.3 66.5 + - - +
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Residues in contact with LYS 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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891 ILE* 3.8 23.1 - - + +
901 ILE 3.2 9.4 - - - +
911 GLU* 4.1 28.5 + - - -
1371 VAL 3.7 1.2 - - - +
1381 VAL* 3.4 4.3 - - - +
1391 THR* 3.0 34.2 + - - +
2551 THR* 5.5 3.6 - - + -
2561 SER* 1.3 77.8 - - - +
2581 VAL* 1.3 63.2 + - - +
2591 ARG* 3.8 28.9 + - - +
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Residues in contact with VAL 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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881 ALA 3.8 0.7 - - - +
891 ILE* 3.4 2.8 - - - -
901 ILE* 2.8 47.7 + - + +
921 VAL* 4.8 4.5 - - + -
1361 PHE* 4.1 26.5 - - + -
1371 VAL 3.6 3.4 - - - -
1381 VAL* 4.0 27.6 - - + -
1551 TYR* 4.8 7.6 - - + -
1571 ILE* 4.5 9.9 - - + -
2431 VAL* 4.0 26.2 - - + -
2571 LYS* 1.3 76.6 - - - +
2591 ARG* 1.3 62.5 + - - +
2601 ILE* 4.1 9.4 + - + +
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Residues in contact with ARG 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* 4.5 4.9 - - - -
881 ALA 3.4 4.5 - - - +
891 ILE* 4.0 39.2 - - + +
1361 PHE* 3.5 4.7 - - - +
1371 VAL* 2.9 44.0 + - + +
1391 THR* 3.8 16.1 + - - +
2571 LYS* 3.8 32.5 + - - +
2581 VAL* 1.3 73.2 - - - +
2601 ILE* 1.3 61.0 + - - +
2611 TYR* 3.6 32.1 - - + +
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Residues in contact with ILE 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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861 CYS* 3.5 3.8 - - - -
871 VAL* 2.9 43.5 + - + +
881 ALA* 3.1 14.2 + - + +
901 ILE* 3.6 28.7 - - + -
1081 TRP* 3.7 11.7 - - + -
1341 PHE* 3.6 32.3 - - + -
1351 THR 3.7 4.0 - - - +
1361 PHE* 3.8 20.0 - - + -
2411 LEU* 3.7 23.6 - - + -
2431 VAL* 6.2 0.4 - - + -
2581 VAL* 4.3 7.4 - - + +
2591 ARG* 1.3 77.9 - - - +
2611 TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 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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841 GLY* 4.2 20.2 - - - -
851 ALA 3.2 7.4 - - - +
861 CYS* 3.5 34.9 - - + +
1331 GLU 3.6 1.2 - - - +
1341 PHE* 3.4 6.6 - - - +
1351 THR* 2.9 52.5 + - + +
1371 VAL* 3.6 30.5 - - + +
2591 ARG* 3.6 39.0 - - + -
2601 ILE* 1.3 75.1 - - - +
2621 MET* 1.3 60.1 + - - +
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Residues in contact with MET 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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831 ARG 3.5 1.6 - - - +
841 GLY* 4.2 0.7 - - - -
851 ALA* 3.0 31.4 + - - +
871 VAL* 3.7 28.9 - - + +
1081 TRP* 4.2 2.0 - - + -
1101 ILE* 4.0 15.5 - - + -
1111 THR* 3.8 22.2 - - - +
1121 TYR* 4.4 12.3 - - + -
1181 LEU* 4.1 12.2 - - + +
1321 MET* 3.5 31.4 - - + -
1331 GLU 3.5 3.8 - - - -
1341 PHE* 3.8 35.2 - - + -
2601 ILE 4.2 0.2 + - - -
2611 TYR* 1.3 74.0 - - - +
2631 LYS* 1.3 59.0 + - - +
2641 PRO* 4.2 3.3 - - - +
10001 SPH 5.0 6.3 - - + -
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Residues in contact with LYS 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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811 PHE 3.9 2.2 - - - +
821 ALA* 3.7 13.0 + - + +
831 ARG* 3.5 37.5 - - - +
841 GLY* 4.1 4.0 - - - +
1321 MET* 3.7 2.4 - - - +
1331 GLU* 3.0 72.0 + - - +
1931 ARG* 5.5 2.4 - - - +
2621 MET* 1.3 72.9 - - - +
2641 PRO* 1.3 74.1 - - - +
2651 LYS* 3.6 14.5 + - + +
434 LYS* 6.0 2.0 - - - +
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Residues in contact with PRO 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* 4.6 1.7 - - - +
811 PHE* 3.7 39.5 - - + +
821 ALA* 4.9 1.6 - - - -
831 ARG 4.7 0.9 - - - +
1181 LEU* 4.6 14.4 - - + -
1221 LEU* 4.6 12.6 - - + -
1301 PHE* 3.8 21.5 - - + -
1311 ASP 3.6 7.4 - - - +
1321 MET* 3.9 16.5 - - + -
2621 MET 4.2 4.7 - - - +
2631 LYS* 1.3 91.8 - - - +
2651 LYS* 1.3 59.7 + - - +
2671 VAL* 3.7 18.0 - - + +
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Residues in contact with LYS 265 (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* 3.6 10.3 - - - +
1301 PHE* 3.7 0.7 - - - +
1311 ASP* 2.9 44.4 + - + +
1331 GLU* 4.2 24.8 + - + +
1951 SER* 2.9 27.2 + - - -
2631 LYS* 4.3 18.6 - - + +
2641 PRO* 1.3 75.8 - - - +
2661 HIS* 1.3 77.2 + - + +
2671 VAL* 3.4 2.5 - - - -
374 ALA 3.0 18.9 + - - -
384 SER 3.7 6.3 + - - -
394 ASN 2.9 27.3 + - - +
404 ALA* 4.8 5.7 - - - +
414 ALA* 4.9 4.9 - - + +
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Residues in contact with HIS 266 (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* 2.9 17.7 + - - -
1291 ARG 3.6 9.0 - - - +
1301 PHE* 3.6 4.5 - - - -
1311 ASP* 2.7 27.5 + - - +
2651 LYS* 1.3 83.3 + - + +
2671 VAL* 1.3 60.5 + - - +
2681 ARG* 4.0 3.6 + - - +
364 SER 3.6 17.4 + - - -
394 ASN* 3.2 25.7 + - + +
404 ALA 2.8 25.7 + - - -
414 ALA* 4.1 10.3 - - - -
424 SER 5.3 1.3 - - - -
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Residues in contact with VAL 267 (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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771 ILE* 3.6 33.0 - - + +
781 GLU* 3.0 23.2 + - - +
811 PHE* 4.1 18.2 - - + -
1221 LEU* 6.2 1.1 - - + -
1291 ARG 3.6 3.6 - - - -
1301 PHE* 4.1 15.5 - - + -
2641 PRO* 3.7 39.3 - - + +
2651 LYS* 3.8 1.6 - - - -
2661 HIS* 1.3 74.2 - - - +
2681 ARG* 1.3 68.3 + - - +
2691 VAL* 4.1 13.9 - - + -
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Residues in contact with ARG 268 (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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771 ILE* 5.0 1.3 - - - -
1281 SER* 3.3 3.6 - - - -
1291 ARG* 2.9 47.9 + - + +
2661 HIS 5.0 3.6 - - - +
2671 VAL* 1.3 77.8 - - - +
2691 VAL* 1.3 64.0 + - - +
2701 TRP* 3.5 46.3 - - + +
464 TYR* 5.8 2.0 + - - -
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Residues in contact with VAL 269 (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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771 ILE* 3.6 38.6 - - + -
811 PHE* 4.5 5.4 - - + -
1221 LEU* 6.0 0.9 - - + -
1251 PHE* 3.6 39.3 - - + -
1271 TYR 3.5 4.7 - - - +
1281 SER* 4.0 16.2 - - - -
2071 HIS* 5.4 1.1 - - + -
2671 VAL* 4.1 14.6 - - + -
2681 ARG* 1.3 79.4 - - - +
2701 TRP* 1.3 70.2 + - - +
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Residues in contact with TRP 270 (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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1251 PHE* 3.7 4.5 - - - +
1261 THR 3.1 16.3 + - - -
1271 TYR* 3.0 46.2 + + + +
1281 SER 4.0 1.8 - - - -
1291 ARG* 3.7 36.6 - - + -
2031 ASN 5.3 0.7 - - - -
2041 ALA* 4.2 10.1 - - + -
2681 ARG* 3.5 57.2 - - + +
2691 VAL* 1.3 81.2 - - - +
2711 CYS* 1.3 76.8 + - - +
2721 PRO* 4.5 0.2 - - - -
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Residues in contact with CYS 271 (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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1251 PHE* 4.4 0.7 - - - -
1261 THR* 2.9 41.6 + - - +
1271 TYR* 4.2 8.1 - - - -
2701 TRP* 1.3 77.8 - - - +
2721 PRO* 1.3 75.5 - - - +
352 TYR* 3.9 36.6 - - - +
1282 PRO* 4.1 5.4 - - + -
2122 VAL* 3.9 24.0 - - - -
534 PHE* 5.4 1.6 - - - -
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Residues in contact with PRO 272 (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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1241 PHE* 3.2 12.8 - - + +
1251 PHE* 4.1 15.9 - - + -
2711 CYS* 1.3 90.0 - - - +
2731 ARG* 1.3 58.3 + - - +
352 TYR* 4.6 4.3 + - + -
1912 VAL* 3.8 22.8 - - + +
1922 TYR* 3.4 21.1 - - - -
534 PHE* 3.6 42.4 - - + -
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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
------------------------------------------------------------
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