Contacts of the strand formed by residues 1445 - 1456 (chain P) in PDB entry 1YYL
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 CYS1445 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1294P ILE 3.8 2.3 - - - +
1295P ASN* 3.5 1.4 - - - -
1296P CYS* 2.9 41.6 + - + +
1376P PHE* 4.1 11.4 - - + -
1378P CYS* 2.0 51.1 - - + -
1383P PHE* 4.3 9.9 - - + -
1444P ARG* 1.3 87.9 - - - +
1446P SER* 1.3 63.4 + - - +
1447P SER* 3.7 18.2 - - - -
1762P NAG 4.2 1.1 - - - -
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Residues in contact with SER1446 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293P VAL* 4.7 3.6 - - - +
1294P ILE 3.7 0.4 - - - -
1295P ASN* 2.6 26.5 + - - -
1444P ARG* 4.3 5.0 - - - +
1445P CYS* 1.3 73.8 - - - +
1447P SER* 1.3 70.4 + - - +
1762P NAG 3.3 32.0 + - - +
1795P NAG 3.4 29.4 + - - -
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Residues in contact with SER1447 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261P LEU* 3.9 27.1 - - - +
1262P ASN* 3.5 13.0 - - - -
1293P VAL* 3.5 5.6 - - - +
1294P ILE* 2.9 42.4 + - - +
1376P PHE* 5.1 0.5 - - - -
1445P CYS* 3.7 11.6 - - - -
1446P SER* 1.3 81.9 + - - +
1448P ASN* 1.3 64.5 + - - +
1762P NAG 3.3 16.8 + - - -
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Residues in contact with ASN1448 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252P ARG* 5.4 5.1 - - - +
1261P LEU* 3.3 3.9 - - - -
1262P ASN* 2.8 40.8 + - - +
1291P SER* 3.3 32.4 + - - +
1292P VAL 3.9 0.9 - - - -
1293P VAL* 3.1 27.9 - - - +
1447P SER* 1.3 73.2 - - - +
1449P ILE* 1.3 60.3 + - - +
1450P THR* 3.1 12.8 + - + +
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Residues in contact with ILE1449 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259P LEU* 3.8 27.1 - - + -
1260P LEU 3.5 7.4 - - - +
1261P LEU* 3.8 15.5 - - + -
1288P LEU* 3.1 26.5 - - + +
1291P SER* 3.6 3.3 - - - -
1292P VAL* 2.9 40.4 + - + +
1294P ILE* 4.0 13.2 - - + -
1333P LEU* 3.6 30.3 - - + -
1338P TRP* 3.7 17.7 - - + -
1448P ASN* 1.3 69.6 - - - +
1450P THR* 1.3 59.3 + - - +
1451P GLY 3.8 18.8 - - - +
1452P LEU* 4.7 0.4 - - + -
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Residues in contact with THR1450 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260P LEU* 2.9 16.9 + - - +
1262P ASN* 3.8 2.9 - - - -
1263P GLY* 3.0 54.6 + - - +
1264P SER 4.1 4.7 + - - -
1265P LEU* 3.5 22.9 - - + -
1287P GLN* 3.7 4.3 - - - +
1288P LEU* 2.6 38.0 + - - +
1291P SER* 4.7 0.7 - - - +
1448P ASN* 3.4 18.6 - - + +
1449P ILE* 1.3 75.5 - - - +
1451P GLY* 1.3 54.4 + - - +
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Residues in contact with GLY1451 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259P LEU* 3.7 1.7 - - - -
1260P LEU* 2.8 39.8 + - - +
1286P VAL 3.0 15.3 - - - -
1287P GLN* 4.4 0.4 - - - -
1288P LEU* 4.1 6.9 - - - +
1449P ILE* 3.6 4.6 - - - +
1450P THR* 1.3 84.1 + - - +
1452P LEU* 1.3 69.8 + - - +
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Residues in contact with LEU1452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258P GLN 3.4 9.9 - - - +
1259P LEU* 4.2 5.2 - - + -
1260P LEU* 4.1 3.0 - - - +
1284P ILE 3.7 0.2 - - - +
1285P ILE* 3.6 4.5 - - - +
1286P VAL* 2.7 49.6 + - + +
1288P LEU* 4.2 14.4 - - + -
1338P TRP* 4.0 23.3 - - + -
1342P LEU* 5.5 1.8 - - + -
1345P ILE* 4.0 27.8 - - + -
1361P PHE* 6.4 0.4 - - + -
1391P PHE* 3.6 36.8 - - + -
1449P ILE* 4.7 0.4 - - + -
1451P GLY* 1.3 84.4 - - - +
1453P LEU* 1.3 66.0 + - - +
1454P LEU* 4.0 12.8 - - + -
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Residues in contact with LEU1453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257P THR* 4.9 3.4 - - - -
1258P GLN 3.1 18.4 + - - +
1259P LEU 6.0 0.2 - - - +
1260P LEU* 4.3 20.2 - - + -
1283P THR* 4.2 7.4 - - + -
1284P ILE 3.6 3.1 - - - -
1285P ILE* 4.0 29.8 - - + -
1452P LEU* 1.3 79.6 - - - +
1454P LEU* 1.3 57.3 + - - +
1470P PRO* 3.5 3.8 - - - +
1471P GLY* 2.5 33.1 + - - +
1472P GLY* 3.5 35.4 - - - +
1474P ASP 5.3 0.2 - - - +
1477P ASP* 4.2 17.9 - - + +
1478P ASN* 4.0 23.1 - - - +
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Residues in contact with LEU1454 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283P THR* 3.4 5.2 - - - +
1284P ILE* 2.8 46.9 + - + +
1286P VAL* 3.6 27.8 - - + -
1345P ILE* 4.1 9.9 - - + -
1349P LEU* 4.5 11.2 - - + -
1361P PHE* 4.0 36.3 - - + -
1391P PHE* 4.6 16.6 - - + -
1452P LEU* 4.6 11.4 - - + -
1453P LEU* 1.3 77.9 - - - +
1455P THR* 1.3 65.6 + - - +
1468P PHE* 4.3 12.6 - - + -
1469P ARG 3.4 17.0 - - - +
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Residues in contact with THR1455 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280P ASN 5.1 5.8 - - - +
1281P ALA 6.3 1.1 - - - -
1282P LYS 5.3 0.9 - - - -
1283P THR* 4.3 21.5 - - + +
1284P ILE* 5.1 2.0 - - - -
1454P LEU* 1.3 76.9 - - - +
1456P ARG* 1.3 60.8 + - - +
1457P ASP* 4.1 3.9 + - - +
1468P PHE* 3.3 7.3 - - - +
1469P ARG* 3.0 43.5 + - - +
1470P PRO 4.0 6.6 + - - -
1471P GLY* 4.6 11.9 - - - -
1472P GLY 5.6 0.4 - - - +
1018S LYS* 5.7 7.0 - - - +
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Residues in contact with ARG1456 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277P PHE 3.3 20.2 + - - -
1278P THR* 3.6 15.2 + - - +
1280P ASN* 3.3 39.8 + - + +
1282P LYS 5.6 1.0 + - - -
1284P ILE* 4.5 8.4 - - + +
1353P PHE* 3.0 33.6 - - - -
1455P THR* 1.3 74.9 - - - +
1457P ASP* 1.3 56.5 + - - +
1458P GLY* 2.7 37.3 + - - -
1466P GLU* 3.1 34.4 + - + +
1467P ILE 3.5 9.6 - - - +
1468P PHE* 3.4 36.3 - - + -
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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