Contacts of the helix formed by residues 1061 - 1078 (chain A) in PDB entry 1YW2
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 SER1061 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A PHE 3.1 1.5 - - - -
1060A GLN* 1.3 85.5 + - - +
1062A ILE* 1.3 58.7 + - - +
1063A ILE* 3.8 9.2 + - - +
1064A HIS* 3.1 28.7 + - - +
1065A ALA* 2.6 36.4 + - - +
1334A ILE* 3.6 14.2 - - - +
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Residues in contact with ILE1062 (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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1061A SER* 1.3 75.0 - - - +
1063A ILE* 1.3 78.6 + - + +
1065A ALA* 3.2 3.7 + - - +
1066A LYS* 2.9 34.8 + - + +
1331A ASP* 5.2 4.9 - - + -
1332A LEU 2.8 31.4 - - - +
1333A LEU* 4.3 6.3 - - + -
1334A ILE* 3.7 27.2 - - + +
1337A TRP* 4.1 9.5 - - + +
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Residues in contact with ILE1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A TYR* 3.7 19.7 - - - +
1061A SER* 3.9 8.5 - - - +
1062A ILE* 1.3 98.9 - - + +
1064A HIS* 1.3 64.0 + - - +
1066A LYS* 3.8 6.2 + - + +
1067A ARG* 3.4 23.2 + - - +
1070A ARG* 5.4 0.7 + - - -
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Residues in contact with HIS1064 (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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1034A ALA 4.6 7.4 + - - -
1035A TYR* 3.3 50.6 + + - -
1056A SER* 5.2 0.6 - - - -
1057A ARG* 2.8 35.9 + - - +
1058A PRO* 2.8 20.0 - - + +
1060A GLN* 3.1 30.9 + - + +
1061A SER* 3.1 26.2 + - - +
1063A ILE* 1.3 81.3 - - - +
1065A ALA* 1.3 63.1 + - - +
1067A ARG* 3.3 4.0 + - - +
1068A THR* 3.1 19.1 + - - -
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Residues in contact with ALA1065 (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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1058A PRO 3.2 9.6 + - - -
1059A PHE* 4.1 11.7 - - + -
1061A SER 2.6 21.3 + - - +
1062A ILE* 3.2 6.5 + - - +
1064A HIS* 1.3 74.3 - - - +
1066A LYS* 1.3 61.9 + - - +
1067A ARG 3.2 1.2 + - - -
1068A THR* 3.4 4.7 + - - -
1069A TYR* 3.3 18.7 + - - +
1334A ILE* 4.3 15.5 - - + +
1337A TRP* 3.4 30.1 - - + +
1341A THR* 4.4 1.9 + - - -
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Residues in contact with LYS1066 (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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1062A ILE* 2.9 21.2 + - + +
1063A ILE* 4.3 6.5 - - + +
1065A ALA* 1.3 73.4 - - - +
1067A ARG* 1.3 56.6 + - - +
1069A TYR* 3.4 2.5 - - - +
1070A ARG* 2.9 38.7 + - - +
1327A PHE* 3.8 16.8 - - + -
1328A GLU* 2.7 46.6 + - - +
1329A SER 4.5 0.6 + - - -
1330A ARG 2.9 17.6 + - - -
1331A ASP* 5.4 1.2 + - - -
1337A TRP* 3.6 39.4 - - + +
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Residues in contact with ARG1067 (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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1035A TYR* 3.9 59.1 - - + +
1053A LYS* 4.7 4.0 - - - +
1055A LEU* 4.6 6.5 - - - +
1063A ILE* 3.4 15.7 + - + +
1064A HIS 3.3 3.2 + - - +
1065A ALA 3.2 1.0 - - - -
1066A LYS* 1.3 74.7 - - - +
1068A THR* 1.3 69.7 + - - +
1069A TYR 3.1 0.9 - - - -
1070A ARG* 3.6 24.3 - - - +
1071A GLU* 2.5 51.9 + - - +
1169A PHE* 4.2 30.0 - - - +
1170A GLY 5.0 8.9 + - - +
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Residues in contact with THR1068 (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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1055A LEU* 3.5 30.6 - - + +
1058A PRO* 2.9 44.3 + - + +
1059A PHE* 3.9 4.3 - - + -
1064A HIS* 3.1 5.8 + - - -
1065A ALA 3.5 8.5 - - - -
1067A ARG* 1.3 76.5 - - - +
1069A TYR* 1.3 53.0 + - - +
1071A GLU* 3.0 5.7 + - - +
1072A LEU* 2.7 37.0 + - + +
1102A VAL* 4.0 7.4 - - + -
1341A THR* 3.9 22.4 - - + -
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Residues in contact with TYR1069 (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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1065A ALA 3.3 7.8 + - - +
1066A LYS 3.4 8.5 - - - +
1068A THR* 1.3 77.3 - - - +
1070A ARG* 1.3 54.3 + - - +
1072A LEU* 3.8 4.0 - - + -
1073A ARG* 2.6 83.8 + - + +
1327A PHE* 3.5 39.2 - + + +
1337A TRP* 3.6 26.2 - + + -
1340A LEU* 3.4 42.9 - - + +
1341A THR* 3.6 23.1 + - - +
1344A GLU* 4.1 9.2 + - + -
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Residues in contact with ARG1070 (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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1063A ILE 5.4 0.6 + - - -
1066A LYS* 2.9 37.2 + - - +
1067A ARG* 3.6 33.2 - - - +
1068A THR 3.3 0.2 - - - -
1069A TYR* 1.3 75.5 - - - +
1071A GLU* 1.3 58.6 + - - +
1073A ARG* 3.8 1.2 - - - +
1074A LEU* 2.9 29.5 + - - +
1169A PHE* 3.6 30.3 - - + -
1323A TYR* 4.0 2.1 + - - -
1327A PHE* 3.6 19.3 - - + -
1328A GLU* 2.7 43.4 + - - +
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Residues in contact with GLU1071 (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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1053A LYS* 2.8 35.3 + - - +
1055A LEU* 4.0 7.6 - - + +
1067A ARG* 2.5 51.9 + - - +
1068A THR* 3.4 5.6 - - - +
1070A ARG* 1.3 75.7 - - - +
1072A LEU* 1.3 64.7 + - - +
1074A LEU* 3.2 2.4 + - - +
1075A LEU* 3.0 41.0 + - + +
1104A LEU* 3.4 15.1 - - + +
1169A PHE* 3.6 33.4 - - + +
2001A PGJ 5.4 0.7 - - - -
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Residues in contact with LEU1072 (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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1068A THR* 2.7 20.1 + - + +
1069A TYR* 3.9 5.8 - - + +
1071A GLU* 1.3 71.3 - - - +
1073A ARG* 1.3 59.4 + - + +
1075A LEU* 4.7 4.0 - - - -
1076A LYS* 2.9 47.5 + - + +
1086A LEU* 3.8 18.6 - - + -
1089A VAL* 4.2 14.4 - - + -
1102A VAL* 5.1 2.9 - - + -
1104A LEU* 4.4 10.7 - - + +
1341A THR* 3.7 21.5 - - + +
1344A GLU* 3.5 32.1 - - + -
1345A VAL* 3.9 19.5 - - + +
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Residues in contact with ARG1073 (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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1069A TYR* 2.6 80.2 + - + +
1070A ARG* 3.8 3.6 - - - +
1072A LEU* 1.3 73.2 - - + +
1074A LEU* 1.3 63.9 + - - +
1076A LYS* 3.3 6.2 + - - +
1077A HIS* 3.2 13.2 + - - +
1323A TYR* 3.2 36.1 - - - +
1324A ASP* 3.2 36.4 + - - +
1327A PHE* 4.4 7.6 - - + +
1344A GLU* 3.6 40.6 + - + -
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Residues in contact with LEU1074 (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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1070A ARG 2.9 20.9 + - - +
1073A ARG* 1.3 71.9 - - - +
1075A LEU* 1.3 56.4 + - - +
1077A HIS* 2.6 25.7 + - + +
1078A MET* 2.9 41.5 + - + +
1146A ILE* 3.3 42.0 - - + -
1168A ASP* 3.6 35.9 - - + +
1169A PHE* 3.9 18.4 - - + -
1323A TYR* 3.2 16.5 + - + +
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Residues in contact with LEU1075 (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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1071A GLU* 3.0 31.6 + - + +
1072A LEU* 4.0 2.9 - - - +
1074A LEU* 1.3 77.3 - - - +
1076A LYS* 1.3 61.8 + - - +
1077A HIS 3.2 0.5 + - - -
1078A MET* 3.4 15.7 + - - +
1084A ILE* 3.9 38.1 - - + +
1085A GLY* 4.0 7.0 - - - +
1086A LEU* 3.8 38.5 + - + +
1104A LEU* 3.5 34.1 - - + -
1168A ASP* 6.2 3.6 - - + +
1169A PHE* 5.3 5.6 - - + -
2001A PGJ 4.5 10.1 - - + -
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Residues in contact with LYS1076 (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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1072A LEU* 2.9 43.9 + - + +
1073A ARG* 3.9 5.8 - - - +
1075A LEU* 1.3 77.2 - - - +
1077A HIS* 1.3 60.9 + - - +
1079A LYS* 4.0 21.3 + - - +
1086A LEU* 4.0 13.0 - - + -
1344A GLU* 2.8 52.9 + - + +
1347A SER* 3.1 16.8 + - - -
1348A PHE* 3.5 29.7 - - + +
1349A VAL 5.4 0.2 - - - +
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Residues in contact with HIS1077 (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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1073A ARG 3.2 5.6 + - - +
1074A LEU* 2.6 19.1 + - + +
1076A LYS* 1.3 75.4 - - - +
1078A MET* 1.3 83.2 - - + -
1079A LYS* 3.2 15.6 + - - +
1140A TYR* 3.4 9.9 + - - -
1144A ALA* 4.6 2.9 - - + -
1320A ALA* 4.6 0.4 - - + +
1321A ASP* 2.6 45.0 + - + -
1322A PRO 3.3 15.5 - - - -
1323A TYR* 3.5 39.8 - + + +
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Residues in contact with MET1078 (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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1074A LEU* 2.9 44.6 + - + +
1075A LEU* 3.4 6.7 + - - +
1077A HIS* 1.3 110.0 - - + +
1079A LYS* 1.3 62.4 + - - +
1080A HIS 3.9 2.1 + - - -
1083A VAL* 3.8 16.7 - - + +
1084A ILE 3.6 18.6 - - - +
1085A GLY* 3.4 22.1 + - - -
1086A LEU 4.7 0.3 + - - -
1140A TYR* 3.3 31.4 - - + -
1141A ILE* 4.2 21.3 - - - -
1144A ALA* 4.8 5.2 - - + -
1146A ILE* 4.6 7.9 - - + -
1168A ASP* 4.6 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
------------------------------------------------------------
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