Contacts of the helix formed by residues 1039 - 1054 (chain D) in PDB entry 6GHM
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 GLY1039 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003D ASN* 3.7 8.3 - - - +
1005D VAL* 5.5 0.7 - - - +
1038D GLU* 1.3 75.3 - - - +
1040D TYR* 1.3 63.2 + - - +
1041D THR 3.4 2.9 - - - -
1042D GLN* 3.6 7.8 + - - +
1043D CYS* 3.1 27.2 + - - +
1202D EDO 3.9 10.3 - - - -
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Residues in contact with TYR1040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003D ASN* 3.5 8.7 - - - +
1033D CYS* 3.8 28.5 - - + -
1034D GLU 3.3 30.1 - - - +
1035D GLU* 3.6 35.3 - - + +
1037D GLU 3.3 10.5 + - - +
1038D GLU 3.2 2.8 + - - -
1039D GLY* 1.3 77.8 - - - +
1041D THR* 1.3 65.4 + - - +
1044D SER* 2.6 54.4 + - - -
1048D TYR* 6.0 1.4 - + - -
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Residues in contact with THR1041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039D GLY 3.4 0.4 - - - -
1040D TYR* 1.3 87.8 - - - +
1042D GLN* 1.3 63.6 + - - +
1044D SER* 3.4 4.2 + - - -
1045D GLN* 3.0 56.5 + - - +
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Residues in contact with GLN1042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005D VAL* 3.8 31.2 - - + +
1039D GLY* 3.6 8.9 + - - +
1040D TYR 3.4 0.2 - - - -
1041D THR* 1.3 80.2 - - - +
1043D CYS* 1.3 57.1 + - - +
1045D GLN* 3.9 6.3 - - - +
1046D PHE* 3.0 28.9 + - + +
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Residues in contact with CYS1043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000D ALA* 4.2 1.6 - - - -
1003D ASN* 3.6 34.8 - - + +
1004D ASN 3.7 1.1 - - - -
1005D VAL* 3.7 17.9 - - + +
1008D CYS* 3.6 30.5 - - - -
1033D CYS* 3.8 14.6 - - - -
1039D GLY 3.1 19.3 + - - +
1040D TYR 4.2 0.9 - - - +
1042D GLN* 1.3 78.3 - - - +
1044D SER* 1.3 62.6 + - - +
1046D PHE* 3.4 2.4 + - - +
1047D LEU* 3.1 23.8 + - - +
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Residues in contact with SER1044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030D ALA 4.7 0.2 - - - -
1033D CYS* 3.7 23.1 - - - -
1040D TYR* 2.6 41.5 + - - -
1041D THR* 3.4 5.2 + - - -
1043D CYS* 1.3 77.5 - - - +
1045D GLN* 1.3 62.5 + - - +
1047D LEU* 4.8 1.6 - - - -
1048D TYR* 2.8 55.3 + - - -
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Residues in contact with GLN1045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041D THR* 3.0 43.3 + - + +
1042D GLN* 4.1 4.9 + - - +
1044D SER* 1.3 76.3 - - - +
1046D PHE* 1.3 60.9 + - - +
1048D TYR* 4.8 3.1 - - - -
1049D GLY* 2.9 27.0 + - - +
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Residues in contact with PHE1046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005D VAL* 3.7 23.6 - - + -
1008D CYS* 4.0 6.7 - - + -
1009D LYS* 3.6 41.3 - - + -
1012D VAL* 4.3 11.0 - - + -
1042D GLN* 3.0 18.9 + - + +
1043D CYS 3.6 3.1 - - - +
1044D SER 3.3 0.2 - - - -
1045D GLN* 1.3 78.0 - - - +
1047D LEU* 1.3 81.8 + - + +
1049D GLY* 3.3 1.4 + - - -
1050D VAL* 2.8 55.1 + - + +
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Residues in contact with LEU1047 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996D LEU* 4.4 19.5 - - + -
1000D ALA* 3.6 31.2 - - + -
1008D CYS* 3.9 18.8 - - + -
1012D VAL* 4.6 5.6 - - + -
1018D VAL* 4.9 4.1 - - + +
1029D ALA* 3.8 4.9 - - + -
1030D ALA* 3.6 32.8 - - + +
1033D CYS* 4.2 7.4 - - - -
1043D CYS 3.1 12.4 + - - +
1044D SER 4.1 1.1 - - - +
1046D PHE* 1.3 98.6 - - + +
1048D TYR* 1.3 61.9 + - - +
1050D VAL* 3.2 6.5 + - + +
1051D GLN* 2.9 32.0 + - - +
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Residues in contact with TYR1048 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030D ALA* 3.6 26.9 + - + -
1031D ASP* 2.4 37.1 + - - -
1040D TYR* 6.0 1.6 - - - -
1044D SER* 2.8 40.5 + - - +
1045D GLN* 4.5 2.7 - - - +
1047D LEU* 1.3 72.2 - - - +
1049D GLY* 1.3 57.7 + - - +
1051D GLN* 3.1 22.5 + - - +
1052D GLU* 2.9 42.9 + - + +
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Residues in contact with GLY1049 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1045D GLN 2.9 21.4 + - - -
1046D PHE 3.6 1.6 - - - -
1047D LEU 3.2 0.2 - - - -
1048D TYR* 1.3 77.4 - - - +
1050D VAL* 1.3 56.3 + - - +
1052D GLU* 3.2 15.6 + - - +
1053D LYS* 3.0 33.4 + - - +
1057D MET* 4.4 0.4 - - - +
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Residues in contact with VAL1050 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012D VAL* 4.7 4.9 - - + -
1018D VAL* 3.7 32.5 - - + -
1046D PHE* 2.8 53.6 + - + +
1047D LEU* 3.2 7.8 + - + +
1049D GLY* 1.3 70.0 - - - +
1051D GLN* 1.3 61.3 + - - +
1054D MET* 2.9 36.9 + - - +
1057D MET* 4.0 13.9 - - + -
1116D LEU* 4.2 23.6 - - + -
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Residues in contact with GLN1051 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018D VAL* 3.7 24.5 + - + +
1019D PHE* 3.4 33.9 - - + -
1028D THR* 2.8 40.7 + - - +
1030D ALA* 3.6 17.1 - - - +
1047D LEU* 2.9 15.7 + - - +
1048D TYR* 3.4 26.1 - - + +
1050D VAL* 1.3 76.0 - - - +
1052D GLU* 1.3 58.6 + - + +
1089D ARG* 3.1 27.7 + - - -
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Residues in contact with GLU1052 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048D TYR* 2.9 29.2 + - + +
1049D GLY* 3.5 11.6 - - - +
1050D VAL 3.1 0.2 - - - -
1051D GLN* 1.3 79.1 - - + +
1053D LYS* 1.3 71.5 + - + +
1056D ILE* 3.8 11.4 - - - +
1089D ARG* 3.1 22.6 + - - +
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Residues in contact with LYS1053 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049D GLY* 3.0 14.8 + - - +
1052D GLU* 1.3 89.2 - - + +
1054D MET* 1.3 59.5 + - - +
1056D ILE* 2.9 27.2 + - + +
1057D MET* 2.9 60.8 + - + +
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Residues in contact with MET1054 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018D VAL* 3.8 30.3 - - + -
1019D PHE* 3.9 15.0 - - + -
1050D VAL* 2.9 21.3 + - + +
1051D GLN 4.2 2.2 - - - +
1052D GLU 3.3 1.4 - - - -
1053D LYS* 1.3 76.5 - - - +
1055D GLY* 1.3 57.9 + - - +
1057D MET* 3.8 6.3 - - - +
1062D ILE* 3.4 28.3 - - + -
1089D ARG* 2.4 37.4 + - - +
1098D TRP* 3.6 19.1 - - + -
1114D LEU* 3.4 43.1 - - + +
1115D GLY* 3.7 7.4 - - - -
1116D LEU* 4.6 6.1 - - + -
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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