Contacts of the helix formed by residues 1039 - 1053 (chain U) in PDB entry 6FF7
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 CYS1039 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852U VAL* 5.1 8.5 - - + -
853U THR 2.7 18.3 + - - +
854U HIS* 4.8 3.7 - - - +
1038U THR* 1.3 72.9 - - - +
1040U THR* 1.3 62.6 + - - +
1042U ALA* 3.4 9.3 + - - +
1043U ALA* 3.0 23.6 + - - +
1067U ILE* 5.0 12.3 - - + -
1071U GLU* 3.7 36.6 - - + +
1074U ILE* 6.1 0.2 - - - +
1075U PRO* 6.3 0.7 - - + -
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Residues in contact with THR1040 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854U HIS 5.5 2.0 + - - -
1038U THR* 3.1 9.7 - - - -
1039U CYS* 1.3 77.8 - - - +
1041U HIS* 1.3 63.2 + - - +
1043U ALA* 3.2 8.9 + - - +
1044U LEU* 3.1 21.6 + - - +
1071U GLU* 6.2 0.4 - - - -
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Residues in contact with HIS1041 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879U LEU* 5.3 1.8 - - + -
880U GLY* 4.9 16.8 - - - +
881U HIS* 5.3 5.4 - - + +
1037U MET* 4.3 9.6 - - + -
1038U THR* 3.2 22.9 + - - +
1040U THR* 1.3 77.7 - - - +
1042U ALA* 1.3 58.1 + - - +
1044U LEU* 3.2 7.4 + - - +
1045U LYS* 2.9 35.1 + - + +
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Residues in contact with ALA1042 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852U VAL* 5.7 3.4 - - + -
1037U MET* 5.0 6.7 - - + +
1038U THR 2.9 15.7 + - - +
1039U CYS* 3.6 10.5 - - - +
1040U THR 3.2 0.2 - - - -
1041U HIS* 1.3 76.4 - - - +
1043U ALA* 1.3 62.9 + - - +
1045U LYS* 5.0 2.0 - - - -
1046U ARG* 3.2 26.7 + - - +
1071U GLU 6.1 0.4 - - - +
1074U ILE* 5.5 3.6 - - + +
1075U PRO* 4.8 22.4 - - + -
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Residues in contact with ALA1043 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668U ALA 4.7 3.3 - - - +
669U VAL* 5.1 15.9 - - + -
672U THR* 3.9 23.7 - - - -
1039U CYS 3.0 13.8 + - - +
1040U THR* 3.2 10.9 + - - +
1042U ALA* 1.3 78.7 - - - +
1044U LEU* 1.3 61.6 + - - +
1045U LYS 3.6 0.2 + - - -
1046U ARG* 3.9 5.9 + - - +
1071U GLU* 5.5 7.9 - - + -
1074U ILE* 5.0 15.9 - - + +
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Residues in contact with LEU1044 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529U GLU* 5.2 6.8 - - - +
668U ALA* 5.2 17.9 - - + +
1040U THR 3.1 12.1 + - - +
1041U HIS* 3.7 9.9 - - - +
1043U ALA* 1.3 78.0 - - - +
1045U LYS* 1.3 60.2 + - + +
1046U ARG 3.5 0.6 + - - -
1047U HIS* 4.8 2.6 + - - +
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Residues in contact with LYS1045 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041U HIS* 2.9 17.9 + - + +
1042U ALA* 3.9 2.7 - - - +
1044U LEU* 1.3 76.2 - - + +
1046U ARG* 1.3 65.7 + - - +
1047U HIS 3.2 3.1 - - - -
1048U ASP* 3.2 13.0 + - + +
1049U LEU* 2.9 25.0 + - + +
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Residues in contact with ARG1046 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672U THR* 5.1 10.3 - - - -
1042U ALA 3.2 17.9 + - - +
1043U ALA* 3.9 8.3 + - - +
1044U LEU 3.5 2.8 - - - -
1045U LYS* 1.3 76.1 - - - +
1047U HIS* 1.3 64.2 + - - +
1049U LEU* 3.2 7.1 + - - +
1050U VAL* 3.0 25.3 + - - +
1074U ILE* 5.7 7.9 - - + +
1077U LEU 5.1 10.1 - - - +
1078U LEU* 4.9 10.1 - - + +
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Residues in contact with HIS1047 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527U ILE 2.6 19.2 - - - +
528U GLY* 3.4 6.1 - - - -
529U GLU* 2.0 65.5 - - + +
672U THR* 6.1 0.6 - - - -
1044U LEU 4.8 1.0 + - - +
1045U LYS 3.2 0.8 - - - -
1046U ARG* 1.3 79.7 - - - +
1048U ASP* 1.3 54.4 + - - +
1050U VAL* 3.4 4.6 + - - +
1051U LYS* 3.1 12.5 + - - +
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Residues in contact with ASP1048 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M GLU* 4.3 3.3 - - + +
526U ASN* 2.9 29.2 - - + -
527U ILE 3.2 10.8 - - - +
529U GLU* 3.9 2.2 - - + +
1045U LYS* 3.2 15.7 + - + +
1047U HIS* 1.3 78.2 - - - +
1049U LEU* 1.3 58.3 + - - +
1051U LYS* 3.3 2.6 + - - +
1052U LEU* 2.9 29.5 + - - +
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Residues in contact with LEU1049 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045U LYS* 2.9 19.1 + - + +
1046U ARG* 3.6 7.4 - - - +
1048U ASP* 1.3 77.9 - - - +
1050U VAL* 1.3 60.7 + - - +
1052U LEU* 3.3 5.7 + - - +
1053U GLY 3.3 3.3 + - - -
1054U PHE* 3.0 40.0 + - + +
1078U LEU* 4.0 18.4 - - + +
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Residues in contact with VAL1050 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M VAL 4.1 1.0 - - - +
205M ASN* 2.9 24.3 + - - +
528U GLY* 5.9 1.1 - - - -
1046U ARG 3.0 16.1 + - - +
1047U HIS* 3.9 5.2 - - - +
1049U LEU* 1.3 75.8 - - - +
1051U LYS* 1.3 57.9 + - - +
1053U GLY 3.1 0.5 + - - -
1054U PHE 5.0 0.9 - - - +
1077U LEU 5.5 2.7 - - - +
1078U LEU 4.0 14.7 + - - +
1079U GLN* 5.0 10.3 - - - +
1080U ASN* 5.4 6.2 + - + +
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Residues in contact with LYS1051 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M VAL 2.9 9.5 - - - +
205M ASN* 1.0 54.1 - - - +
206M ASP* 3.8 0.5 - - - +
207M GLU* 3.4 7.7 + - - -
527U ILE* 2.1 62.2 - - + +
528U GLY* 3.3 5.3 - - - +
1047U HIS 3.1 5.4 + - - +
1048U ASP 3.6 1.6 - - - +
1049U LEU 3.3 0.2 - - - -
1050U VAL* 1.3 70.4 - - - +
1052U LEU* 1.3 48.6 - - - +
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Residues in contact with LEU1052 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M THR 4.3 0.5 - - - +
205M ASN 1.9 13.7 - - - -
206M ASP* 1.6 51.2 + - - +
207M GLU* 3.0 13.9 - - + +
1025U LYS* 6.2 2.0 - - + -
1029U VAL* 4.6 12.0 - - + +
1048U ASP 2.9 14.8 + - - +
1049U LEU* 3.6 8.5 - - - +
1050U VAL 3.2 0.2 - - - -
1051U LYS* 1.3 67.5 - - - +
1053U GLY* 1.3 54.9 - - - +
1054U PHE* 4.3 4.9 - - + +
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Residues in contact with GLY1053 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M THR* 4.0 12.0 - - - +
205M ASN* 0.6 75.1 - - - +
206M ASP 3.0 0.4 - - - -
1029U VAL* 5.0 9.8 - - - +
1050U VAL 3.1 2.2 + - - -
1052U LEU* 1.3 72.5 - - - +
1054U PHE* 1.3 66.2 + - - +
1055U LYS* 3.3 8.0 + - - +
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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