Contacts of the helix formed by residues 1063 - 1079 (chain A) in PDB entry 1Y1V
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 MET1063 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A GLU 4.0 18.2 - - - +
847A ASP 4.8 4.0 - - - -
848A ILE 4.5 0.7 - - - +
849A MET* 3.3 37.9 - - + +
1061A GLY 3.0 2.7 + - - +
1062A GLU* 1.3 67.2 - - - +
1064A VAL* 1.3 63.2 + - - +
1065A GLY 3.3 2.0 - - - -
1066A VAL* 3.7 6.3 + - + +
1067A LEU* 3.2 18.6 + - - +
1424A VAL* 4.2 6.5 - - + -
1435A PRO 4.6 0.7 - - - +
1436A ILE* 3.2 48.7 - - + -
1437A GLY 4.7 0.4 - - - +
1139B ILE* 2.9 37.5 - - + +
1140B ALA* 4.5 11.3 + - - +
1142B GLY* 4.8 2.0 - - - -
88F TYR* 5.2 0.8 + - - -
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Residues in contact with VAL1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A ILE* 3.1 4.5 + - + +
849A MET* 5.1 0.4 - - - -
850A VAL* 3.4 31.0 - - + +
856A THR* 5.6 1.3 - - + -
868A TYR* 2.8 51.4 - - + +
1058A VAL* 5.8 0.2 - - + -
1062A GLU* 2.7 22.1 + - + +
1063A MET* 1.3 71.7 - - - +
1065A GLY* 1.3 59.8 + - - +
1067A LEU* 2.7 10.7 + - + -
1068A ALA* 2.5 44.5 + - + +
1366A ARG 5.8 0.2 - - - +
1367A HIS* 4.5 0.9 - - - +
1370A LEU* 4.0 13.5 - - + -
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Residues in contact with GLY1065 (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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845A LEU* 2.8 33.0 - - - +
848A ILE* 2.4 37.9 + - - +
1064A VAL* 1.3 72.4 - - - +
1066A VAL* 1.3 57.2 + - - +
1068A ALA* 3.2 3.1 + - - +
1069A ALA 2.9 22.2 + - - -
1370A LEU* 4.1 6.7 - - - -
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Residues in contact with VAL1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A VAL* 4.9 10.1 - - + +
845A LEU 3.1 1.1 + - - -
846A GLU* 3.6 33.1 + - + +
1063A MET* 3.7 9.1 + - + +
1064A VAL 3.2 0.4 - - - -
1065A GLY* 1.3 71.0 - - - +
1067A LEU* 1.3 68.3 + - - +
1069A ALA* 3.3 6.4 + - - +
1070A GLN* 2.9 31.9 + - + +
1135B ARG* 6.1 0.4 - - - +
1136B ASP* 3.5 32.3 - - + +
1139B ILE* 4.4 22.9 - - + -
1140B ALA* 3.9 15.3 - - + -
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Residues in contact with LEU1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS* 4.6 22.2 - - + +
514A PRO* 3.7 37.7 - - + -
515A GLN* 5.1 0.4 - - + -
868A TYR* 4.8 5.4 - - + +
874A ASP* 5.6 0.9 - - - +
875A ALA* 5.8 0.2 - - + -
1062A GLU* 4.6 15.7 - - - +
1063A MET 3.2 12.7 + - - +
1064A VAL* 2.7 17.6 + - + +
1066A VAL* 1.3 76.0 - - - +
1068A ALA* 1.3 72.2 + - - +
1070A GLN* 3.2 9.4 + - + +
1071A SER* 3.0 34.2 + - - +
1367A HIS* 3.7 15.9 - - + -
1140B ALA* 4.8 8.7 - - + +
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Residues in contact with ALA1068 (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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845A LEU* 4.4 5.6 - - + -
1064A VAL* 2.5 15.7 + - + +
1065A GLY 3.2 9.9 - - - +
1067A LEU* 1.3 77.4 - - - +
1069A ALA* 1.3 66.0 + - - +
1071A SER* 2.8 16.3 + - - -
1072A ILE* 3.4 10.8 + - + +
1367A HIS* 3.4 42.3 + - - +
1370A LEU* 4.2 17.5 - - + -
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Residues in contact with ALA1069 (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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841A LEU* 3.9 8.4 - - - +
842A VAL* 3.4 39.2 - - + +
845A LEU* 3.5 19.6 - - + +
1065A GLY 2.9 15.9 + - - +
1066A VAL* 3.3 11.9 - - - +
1068A ALA* 1.3 73.3 - - - +
1070A GLN* 1.3 67.2 + - - +
1072A ILE* 2.9 16.0 + - - +
1073A GLY* 3.2 9.0 + - - -
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Residues in contact with GLN1070 (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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449A SER 4.8 1.2 + - - -
450A LEU* 3.5 33.3 - - - +
451A HIS* 3.3 3.3 - - + -
452A LYS* 3.1 31.2 + - - +
838A GLN* 4.2 11.6 + - - +
842A VAL* 4.3 5.9 - - + +
1066A VAL* 2.9 30.5 + - + +
1067A LEU* 3.4 11.5 - - + +
1069A ALA* 1.3 77.0 - - - +
1071A SER* 1.3 56.1 + - - +
1072A ILE 3.1 1.2 + - - -
1073A GLY* 3.1 1.0 + - - -
1074A GLU* 2.8 35.6 + - - +
1136B ASP* 4.3 9.5 - - - +
1137B CYS* 3.8 26.3 - - - +
1140B ALA* 4.2 13.0 - - - +
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Residues in contact with SER1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLN* 2.8 49.9 + - - +
1067A LEU* 3.0 22.7 + - - +
1068A ALA 2.8 16.2 + - - -
1070A GLN* 1.3 71.1 - - - +
1072A ILE* 1.3 56.2 - - - -
1075A PRO* 3.0 18.6 - - - +
1363A VAL* 3.9 13.7 - - - +
1367A HIS* 3.8 16.9 + - - -
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Residues in contact with ILE1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A LEU* 3.7 18.6 - - + -
845A LEU* 5.4 0.4 - - + -
1068A ALA* 3.7 17.0 - - + +
1069A ALA* 2.9 7.9 + - - +
1071A SER* 1.3 74.3 - - - +
1073A GLY* 1.3 55.9 + - - +
1075A PRO* 2.7 25.5 - - - +
1076A ALA* 2.7 21.4 + - + +
1101A LEU* 5.5 8.3 - - + -
1352A VAL* 5.4 1.6 - - + -
1356A ILE* 3.6 27.4 - - + +
1363A VAL* 4.9 1.6 - - + -
1367A HIS* 4.4 5.2 - - + +
1368A MET* 4.0 28.3 - - + +
1371A LEU* 3.7 40.2 - - + -
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Residues in contact with GLY1073 (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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838A GLN* 4.0 21.8 - - - +
841A LEU* 3.4 13.5 - - - +
1069A ALA 3.2 5.3 + - - -
1070A GLN 3.1 5.2 + - - -
1072A ILE* 1.3 77.9 - - - +
1074A GLU* 1.3 60.8 + - - +
1076A ALA* 3.3 10.4 - - - +
1077A THR* 2.7 35.8 + - - -
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Residues in contact with GLU1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 4.4 27.3 - - + +
451A HIS* 4.0 39.5 + - + +
515A GLN* 3.8 18.5 + - - +
838A GLN* 4.5 1.0 - - - +
1070A GLN 2.8 19.7 + - - +
1073A GLY* 1.3 77.0 - - - +
1075A PRO* 1.3 80.7 - - + +
1077A THR* 3.2 15.8 + - - -
1078A GLN* 3.2 31.1 + - - +
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Residues in contact with PRO1075 (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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515A GLN* 4.5 2.7 - - - +
1071A SER 3.0 24.5 - - - +
1072A ILE* 2.7 28.3 - - + +
1074A GLU* 1.3 94.5 - - + +
1076A ALA* 1.3 65.6 + - - +
1077A THR 3.1 2.0 - - - -
1078A GLN* 3.0 19.3 + - + +
1079A MET* 3.2 14.5 + - - +
1356A ILE* 4.8 9.6 - - + -
1359A ASP* 5.8 0.5 - - - -
1361A SER* 4.5 23.1 + - - +
1363A VAL* 4.6 10.3 - - + -
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Residues in contact with ALA1076 (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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834A THR* 4.4 5.5 + - + -
837A ILE* 4.4 17.2 - - + +
838A GLN* 5.6 0.7 - - + +
841A LEU* 5.2 0.4 - - + -
1072A ILE* 2.7 21.7 + - + +
1073A GLY* 3.1 14.8 + - - +
1075A PRO* 1.3 77.2 - - - +
1077A THR* 1.3 63.6 + - - +
1079A MET* 3.1 35.4 + - + +
1098A VAL* 4.3 4.3 - - - +
1101A LEU* 4.3 18.4 - - + -
1356A ILE* 6.2 1.3 - - - -
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Residues in contact with THR1077 (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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450A LEU* 4.4 14.4 - - + +
830A LYS* 3.7 16.0 - - - -
834A THR* 3.1 40.6 + - + +
838A GLN* 4.0 10.9 - - - +
1073A GLY 2.7 19.2 + - - -
1074A GLU* 3.3 10.3 + - - -
1076A ALA* 1.3 77.9 - - - +
1078A GLN* 1.3 62.5 + - + +
1079A MET 3.5 0.9 + - - +
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Residues in contact with GLN1078 (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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479A ASN* 5.9 1.8 - - - +
830A LYS* 4.9 1.8 - - - +
1074A GLU* 3.2 36.5 + - - +
1075A PRO* 3.0 11.6 + - + +
1077A THR* 1.3 81.3 - - + +
1079A MET* 1.3 65.7 + - - +
1080A THR* 3.5 2.4 + - - -
1359A ASP* 4.4 0.4 - - - +
286S THR* 3.6 30.7 + - + +
287S ARG* 4.7 20.7 + - - +
307S LYS* 4.1 32.6 + - - +
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Residues in contact with MET1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A LYS* 3.4 19.5 - - - +
834A THR* 5.4 0.2 + - - -
837A ILE* 5.3 1.3 - - + -
1075A PRO* 3.2 11.2 + - + +
1076A ALA* 3.1 22.6 + - + +
1077A THR 4.2 0.5 - - - +
1078A GLN* 1.3 79.5 - - - +
1080A THR* 1.3 66.0 + - - +
1081A LEU* 3.6 3.6 - - - +
1097A GLY* 4.6 3.6 - - - -
1098A VAL* 3.3 32.2 - - + +
1101A LEU* 3.0 41.3 - - + -
1355A VAL* 4.2 23.3 - - - +
1356A ILE* 4.9 6.3 - - + -
1359A ASP* 3.4 26.9 - - - +
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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