Contacts of the helix formed by residues 1039 - 1054 (chain B) in PDB entry 4A63
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ASN* 3.7 11.9 - - - +
1005B VAL* 5.5 1.5 - - - +
1038B GLU* 1.3 73.8 + - - +
1040B TYR* 1.4 62.1 + - - +
1041B THR 3.6 1.6 - - - -
1042B GLN* 3.7 12.2 + - - +
1043B CYS* 3.1 27.2 + - - +
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Residues in contact with TYR1040 (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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1003B ASN* 3.5 8.0 - - - +
1033B CYS* 3.7 35.7 - - + -
1034B GLU 3.3 28.0 - - - +
1035B GLU* 3.7 26.1 - - + +
1037B GLU 3.7 7.8 + - - +
1038B GLU 3.4 3.0 - - - -
1039B GLY* 1.4 72.6 - - - +
1041B THR* 1.4 62.7 + - - +
1043B CYS* 3.1 1.7 + - - +
1044B SER* 2.8 55.0 + - - -
1048B TYR* 5.3 5.0 - - - -
218C GLU* 2.8 31.4 + - + -
219C GLY* 3.8 20.2 - - - +
253C LEU* 3.9 10.3 - - + -
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Residues in contact with THR1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B GLY 3.6 0.2 - - - -
1040B TYR* 1.4 77.6 - - - +
1042B GLN* 1.3 57.8 + - - +
1044B SER* 3.9 4.5 - - - -
1045B GLN* 3.0 37.4 + - + +
218C GLU 4.4 1.4 + - - -
219C GLY 3.8 17.0 + - - -
251C THR* 4.0 36.7 + - + +
253C LEU* 3.8 31.6 + - + +
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Residues in contact with GLN1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B VAL* 3.5 33.6 - - + +
1006B GLN* 5.0 4.9 + - - +
1039B GLY* 3.7 12.9 + - - +
1040B TYR 3.3 0.4 - - - -
1041B THR* 1.3 79.6 - - - +
1043B CYS* 1.3 59.2 + - - +
1045B GLN* 4.3 2.7 - - - +
1046B PHE* 3.3 23.0 + - - +
244C GLN* 3.7 37.6 + - + +
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Residues in contact with CYS1043 (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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1000B ALA* 4.2 2.0 - - - -
1003B ASN* 3.8 15.5 - - + -
1004B ASN 3.7 17.5 - - - -
1005B VAL* 3.8 16.3 - - + +
1008B CYS* 3.7 30.5 - - - -
1033B CYS* 3.8 15.3 - - - -
1039B GLY 3.1 20.3 + - - +
1040B TYR 3.1 2.0 + - - +
1042B GLN* 1.3 75.5 - - - +
1044B SER* 1.3 64.6 + - - +
1046B PHE* 3.3 3.8 + - - +
1047B LEU* 3.1 24.1 + - - +
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Residues in contact with SER1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B ALA 4.4 1.3 - - - -
1033B CYS* 3.8 24.1 - - - -
1040B TYR* 2.8 49.3 + - - -
1041B THR* 3.5 4.9 + - - -
1043B CYS* 1.3 71.3 - - - +
1045B GLN* 1.3 60.6 + - - +
1047B LEU* 3.3 2.2 + - - +
1048B TYR* 2.8 53.9 + - - -
253C LEU* 4.4 5.2 - - - +
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Residues in contact with GLN1045 (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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1041B THR* 3.0 29.6 + - + +
1042B GLN* 4.5 2.7 - - - +
1044B SER* 1.3 82.5 + - - +
1046B PHE* 1.3 56.8 + - - +
1048B TYR* 4.5 12.8 - - - +
1049B GLY* 3.1 24.1 + - - -
132C GLN* 4.2 10.2 + - - +
158C THR* 4.1 14.1 - - - +
160C PRO* 3.3 26.1 - - - +
251C THR* 4.8 5.1 - - + +
253C LEU* 3.6 33.3 - - + +
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Residues in contact with PHE1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B VAL* 4.0 20.9 - - + -
1008B CYS* 4.0 11.4 - - + -
1009B LYS* 3.6 53.2 - - + -
1012B VAL* 4.3 12.1 - - + -
1042B GLN 3.3 18.4 + - - +
1043B CYS 3.3 3.9 + - - +
1044B SER 3.2 0.6 - - - -
1045B GLN* 1.3 78.4 - - - +
1047B LEU* 1.3 75.9 + - + +
1049B GLY* 3.3 2.4 + - - -
1050B VAL* 3.1 46.5 + - + +
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Residues in contact with LEU1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B LEU* 4.3 22.7 - - + -
1000B ALA* 3.7 30.7 - - + -
1008B CYS* 3.9 20.0 - - + -
1012B VAL* 4.5 6.1 - - + -
1018B VAL* 4.3 8.5 - - + +
1029B ALA* 4.0 4.0 - - + -
1030B ALA* 3.5 30.5 - - + +
1033B CYS* 4.2 3.6 - - - -
1043B CYS 3.1 18.8 + - - +
1044B SER 4.0 0.9 - - - +
1046B PHE* 1.3 93.9 - - + +
1048B TYR* 1.4 65.1 + - - +
1050B VAL* 3.3 6.6 + - + +
1051B GLN* 3.1 24.6 + - - +
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Residues in contact with TYR1048 (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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1030B ALA* 3.6 26.6 + - + -
1031B ASP* 2.5 38.3 + - - +
1040B TYR* 5.3 5.4 - - - -
1044B SER* 2.8 39.4 + - - +
1045B GLN* 4.5 14.8 - - - +
1047B LEU* 1.4 71.1 - - - +
1049B GLY* 1.3 57.0 + - - +
1051B GLN* 3.4 20.1 + - + +
1052B GLU* 3.0 49.8 + - - +
158C THR* 6.2 0.2 - - - -
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Residues in contact with GLY1049 (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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1045B GLN 3.1 20.4 + - - -
1046B PHE 3.6 2.5 - - - -
1047B LEU 3.2 0.4 - - - -
1048B TYR* 1.3 77.2 - - - +
1050B VAL* 1.4 49.7 + - - +
1052B GLU* 3.2 8.7 + - - +
1053B LYS* 2.7 54.9 + - - +
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Residues in contact with VAL1050 (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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1012B VAL* 4.6 10.3 - - + -
1018B VAL* 3.8 31.6 - - + -
1046B PHE* 3.1 43.1 + - + +
1047B LEU* 3.3 8.0 + - - +
1049B GLY* 1.4 73.1 - - - +
1051B GLN* 1.4 58.8 + - - +
1053B LYS* 4.5 2.9 - - - +
1054B MET* 2.9 47.0 + - + +
1057B MET* 5.4 5.2 - - - -
1116B LEU* 4.2 21.8 - - + -
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Residues in contact with GLN1051 (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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1018B VAL* 3.6 19.8 + - + +
1019B PHE* 3.3 39.6 - - + -
1028B THR* 2.9 37.8 + - - +
1029B ALA* 5.9 0.2 - - - +
1030B ALA* 3.5 22.0 - - - +
1047B LEU* 3.1 12.3 + - - +
1048B TYR* 3.5 25.6 - - + +
1049B GLY 3.3 0.2 - - - -
1050B VAL* 1.4 76.6 - - - +
1052B GLU* 1.3 57.0 + - + +
1054B MET* 4.6 0.2 - - - +
1089B ARG* 3.2 25.1 + - - -
1111B ARG* 5.1 0.2 + - - -
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Residues in contact with GLU1052 (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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1048B TYR* 3.0 39.0 + - - +
1049B GLY* 3.7 6.6 - - - +
1051B GLN* 1.3 81.5 - - + +
1053B LYS* 1.4 60.8 + - + +
1054B MET 3.6 0.2 - - - -
1056B ILE* 3.7 12.5 - - - +
1089B ARG* 3.4 19.0 + - - +
132C GLN* 4.8 12.0 + - - -
135C SER* 6.1 0.9 - - - +
141C THR* 5.7 1.0 + - - -
142C TRP* 5.8 1.9 + - - -
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Residues in contact with LYS1053 (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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1049B GLY* 2.7 30.7 + - - +
1052B GLU* 1.4 75.1 - - + +
1054B MET* 1.3 62.5 + - - +
1056B ILE* 3.0 11.2 + - + +
1057B MET* 2.9 59.7 + - + +
132C GLN* 6.3 3.3 - - - -
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Residues in contact with MET1054 (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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1018B VAL* 4.0 24.9 - - - -
1019B PHE* 4.1 14.8 - - + -
1050B VAL* 2.9 26.2 + - + +
1051B GLN 4.6 1.8 - - - +
1052B GLU 3.6 1.6 - - - -
1053B LYS* 1.3 73.9 - - - +
1055B GLY* 1.3 57.0 + - - +
1057B MET* 4.8 0.4 - - - -
1062B ILE* 3.4 24.9 - - + -
1089B ARG* 2.5 34.6 + - - +
1098B TRP* 3.4 27.3 - - + -
1114B LEU* 3.9 20.2 - - + +
1115B GLY 3.9 12.8 - - - -
1116B LEU* 3.7 32.3 - - + -
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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