Contacts of the helix formed by residues 1033 - 1044 (chain C) in PDB entry 5D4C
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 GLY1033 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031C ARG* 3.7 10.0 + - - +
1032C PHE* 1.3 76.5 - - - +
1034C GLU* 1.3 65.3 + - - -
1035C MET 3.2 2.0 - - - -
1036C GLU* 2.9 21.3 + - - -
1037C VAL* 3.1 22.5 + - - +
620D GLY* 4.2 4.3 - - - -
14G G 5.2 0.7 - - - -
15G T 3.9 20.8 - - - -
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Residues in contact with GLU1034 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C ARG* 4.7 3.2 - - - +
1033C GLY* 1.3 71.2 - - - -
1035C MET* 1.3 61.5 + - + +
1037C VAL* 3.3 4.2 + - - +
1038C TRP* 2.9 51.1 + - + +
615D ARG* 3.1 54.0 + - - +
619D LEU* 3.8 36.3 + - + +
620D GLY* 4.5 0.8 - - - -
1096D ARG* 3.6 27.3 + - - -
14G G 4.8 5.6 + - - -
15G T 5.1 0.6 + - - -
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Residues in contact with MET1035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033C GLY 3.2 0.4 - - - -
1034C GLU* 1.3 79.1 - - + +
1036C GLU* 1.3 66.1 + - - +
1038C TRP* 3.2 41.0 - - + +
1039C ALA* 2.9 24.1 + - - +
706D PRO* 5.0 2.9 - - - -
707D THR* 3.2 49.4 - - - +
708D LEU* 4.4 15.5 - - + -
1092D GLY* 6.1 3.8 - - - +
1095D THR* 4.9 9.9 - - + -
1227D GLN* 4.5 1.2 + - - -
13G A 4.9 7.9 - - + -
14G G 3.7 41.1 - - - +
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Residues in contact with GLU1036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C ARG 4.9 3.8 - - - +
1032C PHE* 3.6 38.0 - - + -
1033C GLY* 2.9 31.4 + - - +
1034C GLU 3.3 0.2 - - - -
1035C MET* 1.3 80.1 + - - +
1037C VAL* 1.3 59.8 + - - +
1039C ALA* 2.9 23.7 + - - +
1040C LEU* 2.9 18.2 + - - +
703D ASN* 3.1 27.5 - - - +
705D ALA* 4.7 8.8 - - - +
707D THR* 2.9 24.3 + - - +
713D ILE* 4.1 2.2 - - + -
14G G 5.2 2.1 - - - +
15G T 5.1 8.1 - - - +
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Residues in contact with VAL1037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C PHE* 4.2 12.6 - - + -
1033C GLY 3.1 10.3 + - - +
1034C GLU 3.4 8.1 - - - +
1036C GLU* 1.3 76.5 - - - +
1038C TRP* 1.3 59.7 + - + +
1040C LEU* 3.4 1.7 + - - +
1041C GLU* 2.9 55.2 + - - +
1049C LEU* 3.7 30.3 - - + -
1053C LEU* 4.7 7.0 - - + -
619D LEU 3.2 24.2 - - - +
620D GLY* 4.5 3.6 - - - -
1466D VAL* 4.0 16.2 - - + -
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Residues in contact with TRP1038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C GLU* 2.9 40.7 + - + +
1035C MET* 3.2 44.0 - - + +
1036C GLU 3.1 0.2 - - - -
1037C VAL* 1.3 79.4 - - + +
1039C ALA* 1.3 56.1 + - - +
1041C GLU* 4.1 18.6 - - - -
1042C ALA* 2.9 31.7 + - - +
707D THR 5.3 0.9 - - - -
1092D GLY 5.6 0.2 - - - -
1095D THR* 3.9 22.2 - - + -
1096D ARG* 3.7 42.8 - - + -
1099D VAL* 3.3 41.7 - - + +
1223D ILE* 3.5 8.1 - - + +
1227D GLN* 3.4 19.5 + - + +
1463D LYS* 6.2 1.2 - - - +
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Residues in contact with ALA1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C MET 2.9 11.9 + - - +
1036C GLU 2.9 9.9 + - - +
1038C TRP* 1.3 76.3 - - - +
1040C LEU* 1.3 64.2 + - - +
1042C ALA* 3.3 3.1 + - - +
1043C TYR* 3.0 28.4 + - - +
707D THR* 3.9 12.3 - - + -
710D ARG* 3.9 12.4 - - - +
713D ILE* 3.7 32.1 - - + -
1227D GLN* 3.7 7.6 - - - +
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Residues in contact with LEU1040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C PHE* 3.4 37.5 - - + -
1036C GLU 2.9 8.9 + - - +
1037C VAL 3.9 3.6 - - - +
1039C ALA* 1.3 76.6 - - - +
1041C GLU* 1.3 63.9 + - - +
1043C TYR* 3.2 4.6 + - - +
1044C GLY 3.0 15.9 + - - -
1045C ALA* 3.1 17.5 + - + +
1048C THR* 3.9 14.8 - - + -
1049C LEU* 3.7 41.3 - - + +
1052C MET* 4.2 2.2 - - + -
701D LEU* 4.5 6.5 - - + -
713D ILE* 4.4 11.9 - - + -
763D MET* 3.9 34.1 - - + -
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Residues in contact with GLU1041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C VAL* 2.9 33.3 + - - +
1038C TRP* 3.8 12.3 - - - +
1040C LEU* 1.3 76.2 - - - +
1042C ALA* 1.3 55.3 + - - +
1044C GLY* 2.7 24.8 + - - -
1049C LEU* 3.7 15.3 - - + -
1103D HIS* 5.4 0.2 - - - +
1220D ALA* 4.0 14.3 - - - +
1223D ILE* 3.5 20.2 - - + +
1462D LEU* 3.4 37.9 - - + +
1463D LYS* 5.0 2.6 + - - +
1466D VAL* 3.2 27.0 - - - +
1472D ILE* 4.0 13.7 - - + +
1474D ALA* 5.2 0.2 - - - +
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Residues in contact with ALA1042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C TRP 2.9 19.1 + - - +
1041C GLU* 1.3 76.6 - - - +
1043C TYR* 1.3 58.6 + - - +
1044C GLY 3.6 0.2 + - - -
710D ARG* 3.3 31.3 + - + -
1219D GLU* 4.9 2.9 - - - +
1220D ALA 4.6 4.8 + - - +
1223D ILE* 3.9 12.1 - - + +
1224D VAL* 3.8 25.3 - - + +
1227D GLN* 3.2 23.6 - - - +
17E TYR* 4.9 2.6 + - - -
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Residues in contact with TYR1043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039C ALA 3.0 19.5 + - - -
1040C LEU* 3.5 11.0 - - + +
1041C GLU 3.1 0.2 - - - -
1042C ALA* 1.3 77.0 - - - +
1044C GLY* 1.3 59.4 + - - +
1045C ALA 4.2 3.1 - - - +
710D ARG* 2.9 47.6 + - - +
711D LEU* 4.1 5.5 - - - +
713D ILE* 3.0 23.6 + - + -
714D GLN* 3.8 11.8 - - - +
762D GLN* 2.9 38.5 + - + +
763D MET* 3.6 44.9 + - + -
768D ASN* 3.6 29.9 + - - -
17E TYR* 3.4 11.4 + - - -
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Residues in contact with GLY1044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C LEU 3.0 0.2 + - - -
1041C GLU* 2.7 20.0 + - - -
1042C ALA 3.2 0.6 - - - -
1043C TYR* 1.3 79.9 - - - +
1045C ALA* 1.3 59.5 + - - +
1046C ALA 3.7 0.7 - - - -
762D GLN* 3.3 9.2 + - - -
1218D GLY 5.4 0.4 - - - -
1220D ALA 5.6 2.2 - - - -
1472D ILE* 5.2 2.0 - - - -
1474D ALA* 4.5 5.2 - - - -
1475D GLY* 3.2 19.0 - - - -
1476D THR* 3.2 26.0 + - - -
17E TYR* 4.0 4.3 - - - -
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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