Contacts of the helix formed by residues 1035 - 1048 (chain B) in PDB entry 3QCF
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 ALA1035 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033B GLU 4.3 0.8 + - - -
1034B TYR* 1.3 71.4 - - - +
1036B LEU* 1.3 59.5 + - - +
1037B PRO 3.5 0.4 - - - -
1038B VAL* 3.2 6.3 + - - +
1039B LEU* 3.0 31.5 + - + +
1111B PHE* 4.1 15.4 - - + -
1114B ASP* 3.8 18.2 + - - +
1115B ALA* 3.6 34.3 - - + +
1118B GLU* 4.3 15.9 + - + +
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Residues in contact with LEU1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034B TYR* 3.3 2.7 - - + -
1035B ALA* 1.3 76.5 - - - +
1037B PRO* 1.3 74.2 - - + +
1039B LEU* 3.3 21.0 + - + +
1040B THR* 3.2 31.6 + - - +
1043B ARG* 5.1 6.5 - - - +
1118B GLU* 4.3 13.0 + - + +
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Residues in contact with PRO1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988B CYS* 3.6 27.9 - - + +
989B TYR* 5.6 1.4 - - - -
1023B TYR* 3.2 23.4 - - - +
1025B GLN* 4.7 5.2 - - - +
1034B TYR* 3.2 28.7 - - + +
1036B LEU* 1.3 95.7 - - + +
1038B VAL* 1.3 56.1 + - - +
1040B THR* 3.5 8.0 + - - +
1041B PHE* 3.1 25.3 + - - +
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Residues in contact with VAL1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023B TYR* 3.7 16.4 - - - +
1032B PRO* 5.1 2.2 - - + -
1034B TYR 4.3 6.5 - - - +
1035B ALA 3.2 7.6 + - - +
1036B LEU 3.1 0.8 - - - -
1037B PRO* 1.3 72.5 - - - +
1039B LEU* 1.3 56.8 + - + +
1040B THR 3.1 1.6 - - - -
1041B PHE* 3.0 1.8 + - - -
1042B VAL* 2.7 49.6 + - + +
1073B ILE* 4.8 5.2 - - + -
1111B PHE* 3.9 22.0 - - + -
1115B ALA* 5.9 1.1 - - + -
2001B NXY 3.4 63.0 - - + -
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Residues in contact with LEU1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B ALA 3.0 22.5 + - - +
1036B LEU* 3.3 25.8 + - + +
1038B VAL* 1.3 76.0 - - + +
1040B THR* 1.3 58.2 + - - +
1042B VAL* 3.8 5.4 - - - +
1043B ARG* 2.9 54.5 + - - +
1073B ILE* 4.7 7.9 - - + -
1077B LEU* 4.5 13.7 - - + -
1115B ALA* 3.4 39.3 - - + +
1116B LEU* 5.3 0.2 - - - -
1118B GLU* 4.3 9.0 - - + -
1119B ALA* 4.0 28.5 - - + +
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Residues in contact with THR1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989B TYR* 4.7 9.4 - - + -
1036B LEU* 3.2 18.2 + - - +
1037B PRO* 3.5 10.8 - - - +
1038B VAL 3.1 0.4 - - - -
1039B LEU* 1.3 79.8 - - - +
1041B PHE* 1.3 58.0 + - - +
1043B ARG* 3.9 8.8 + - - +
1044B ARG* 3.0 72.4 + - + +
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Residues in contact with PHE1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948B VAL* 3.8 23.8 - - + -
949B MET 4.4 1.6 - - - -
950B ILE* 4.8 1.6 - - + -
989B TYR* 3.5 37.7 - + + -
1021B TYR* 3.5 50.7 - + + -
1022B HIS 3.7 4.3 - - - -
1023B TYR* 3.6 28.3 - + + -
1037B PRO 3.1 11.4 + - - +
1038B VAL 3.0 6.6 + - - +
1040B THR* 1.3 78.4 - - - +
1042B VAL* 1.3 58.3 + - - +
1044B ARG* 4.2 1.1 - - - +
1045B SER* 2.9 36.2 + - - -
1070B TYR* 4.0 9.0 - + - -
2001B NXY 3.3 28.7 - - + -
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Residues in contact with VAL1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B VAL* 2.7 41.6 + - + +
1039B LEU* 3.8 5.2 - - - +
1041B PHE* 1.3 70.4 - - + +
1043B ARG* 1.3 60.9 + - - +
1045B SER* 3.1 5.9 + - - -
1046B SER* 2.8 35.6 + - - -
1070B TYR* 4.0 21.5 - - + -
1073B ILE* 4.2 13.9 - - + -
1074B ASP* 3.8 41.3 - - + +
1077B LEU* 4.2 12.6 - - + -
2001B NXY 4.7 2.5 - - + -
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Residues in contact with ARG1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036B LEU* 5.1 6.5 - - - +
1039B LEU* 2.9 46.6 + - - +
1040B THR* 3.9 7.5 + - - +
1042B VAL* 1.3 79.5 - - - +
1044B ARG* 1.3 59.4 + - + +
1046B SER* 3.9 3.2 - - - -
1047B ALA* 3.0 31.1 + - - +
1077B LEU* 4.2 21.3 - - + +
1119B ALA* 3.3 41.0 + - - +
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Residues in contact with ARG1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986B HIS* 5.7 2.3 + - - -
989B TYR* 3.1 28.5 + - + +
1021B TYR* 4.0 12.3 + - + +
1040B THR* 3.0 40.4 + - + +
1041B PHE 4.2 1.8 - - - +
1043B ARG* 1.3 76.0 - - + +
1045B SER* 1.3 64.1 + - - +
1047B ALA* 3.2 6.0 + - - +
1048B ALA* 3.2 21.3 + - - +
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Residues in contact with SER1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946B ILE* 4.2 11.6 - - - +
948B VAL* 4.3 7.1 - - - +
1021B TYR* 3.6 39.9 - - - -
1041B PHE* 2.9 26.4 + - - -
1042B VAL 3.1 2.3 + - - -
1044B ARG* 1.3 76.9 - - - +
1046B SER* 1.3 61.5 + - - +
1048B ALA* 3.4 14.9 + - - +
1049B ARG* 4.3 2.8 + - - +
1056B VAL* 5.6 2.1 - - - +
1070B TYR* 2.6 34.0 + - - -
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Residues in contact with SER1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042B VAL 2.8 20.3 + - - -
1043B ARG* 3.9 4.3 - - - -
1045B SER* 1.3 77.5 + - - +
1047B ALA* 1.3 62.7 + - - +
1048B ALA 3.1 0.9 + - - -
1049B ARG* 3.4 23.9 - - - +
1056B VAL* 6.4 1.1 - - - -
1070B TYR* 4.1 5.6 - - - -
1074B ASP* 2.9 34.9 + - - -
1078B GLN* 3.8 11.3 + - - +
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Residues in contact with ALA1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043B ARG 3.0 18.8 + - - +
1044B ARG* 3.2 7.2 + - - +
1046B SER* 1.3 72.2 - - - +
1048B ALA* 1.3 57.5 + - - +
1049B ARG 3.0 12.2 + - - +
1050B MET* 3.8 12.3 - - - +
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Residues in contact with ALA1048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946B ILE* 3.5 20.0 - - + +
1019B ILE* 5.7 1.3 - - + -
1021B TYR* 3.3 36.6 - - + +
1044B ARG 3.2 4.7 + - - +
1045B SER 3.5 13.7 - - - +
1046B SER 3.1 0.8 - - - -
1047B ALA* 1.3 76.3 - - - +
1049B ARG* 1.3 59.8 + - - +
1050B MET* 3.3 17.9 + - - +
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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
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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