Contacts of the helix formed by residues 1025 - 1045 (chain C) in PDB entry 4DDI
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 ALA1025 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 5.0 6.0 - - + +
51C PHE* 3.5 35.7 - - + -
145C TYR 5.8 2.0 - - - +
146C ALA 4.4 13.2 - - - +
148C GLY 3.8 13.9 - - - +
149C GLY 3.0 0.2 + - - -
150C SER* 1.3 82.0 + - - +
1026C TYR* 1.3 65.1 + - - +
1027C ASP* 2.7 2.0 + - - -
1028C GLU* 2.8 22.3 + - - +
1029C ALA* 3.8 1.7 + - - +
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Residues in contact with TYR1026 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.1 28.7 + - - -
49C VAL* 4.4 20.8 - - + +
146C ALA 5.6 0.4 + - - -
147C MET* 4.1 35.2 - - + +
148C GLY 4.7 0.2 + - - -
149C GLY* 2.9 13.1 + - - +
150C SER 2.2 11.9 + - - +
1025C ALA* 1.3 71.9 - - - +
1027C ASP* 1.3 66.5 + - - +
1029C ALA* 2.9 12.7 + - + +
1030C ILE* 2.9 42.4 + - + +
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Residues in contact with ASP1027 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 2.7 53.0 + - - +
149C GLY 4.9 0.5 - - - +
150C SER* 2.5 28.8 + - - +
1025C ALA 2.7 1.0 + - - +
1026C TYR* 1.3 72.4 - - - +
1028C GLU* 1.3 52.0 + - - +
1030C ILE* 3.0 13.1 + - - +
1031C MET* 2.6 38.6 + - - +
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Residues in contact with GLU1028 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 4.6 27.7 + - - +
34C GLN* 4.1 16.9 + - - +
36C THR* 4.7 9.4 - - + +
51C PHE* 3.9 27.6 - - + -
1025C ALA* 2.8 15.3 + - - +
1027C ASP* 1.3 73.2 - - - +
1029C ALA* 1.3 52.3 + - - +
1031C MET* 3.0 12.6 + - + +
1032C ALA* 2.7 35.1 + - - +
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Residues in contact with ALA1029 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR* 5.7 7.0 - - - +
38C MET* 4.0 25.8 - - + +
49C VAL* 4.2 22.2 - - + -
51C PHE* 5.7 0.2 - - - -
1025C ALA 3.8 1.8 + - - +
1026C TYR* 2.9 13.4 + - + +
1028C GLU* 1.3 80.3 - - - +
1030C ILE* 1.3 58.7 + - + +
1032C ALA* 3.0 11.0 + - - +
1033C GLN* 2.9 27.9 + - - +
1036C ARG* 4.7 1.9 + - - -
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Residues in contact with ILE1030 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026C TYR* 2.9 43.0 + - + +
1027C ASP* 3.7 12.6 - - - +
1029C ALA* 1.3 74.9 - - + +
1031C MET* 1.3 60.3 + - - +
1033C GLN* 3.4 25.1 - - - +
1034C GLN* 3.3 26.3 - - - +
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Residues in contact with MET1031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.8 41.5 - - + +
64A PRO* 4.0 22.9 - - + -
90A ARG 5.9 2.2 - - - +
1027C ASP 2.6 20.8 + - - +
1028C GLU* 3.3 12.6 - - + +
1030C ILE* 1.3 72.3 - - - +
1032C ALA* 1.3 65.0 + - - +
1034C GLN* 3.0 15.4 + - + +
1035C ASP* 2.9 31.6 + - - +
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Residues in contact with ALA1032 (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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36C THR* 5.8 3.1 - - - +
38C MET* 6.0 1.3 - - + -
1028C GLU 2.7 13.1 + - - +
1029C ALA* 3.2 13.5 - - - +
1031C MET* 1.3 76.8 - - - +
1033C GLN* 1.3 51.2 + - - +
1035C ASP* 3.0 12.8 + - - +
1036C ARG* 2.7 52.6 + - - +
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Residues in contact with GLN1033 (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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1029C ALA 2.9 11.7 + - - +
1030C ILE* 3.4 25.6 - - + +
1032C ALA* 1.3 74.5 - - - +
1034C GLN* 1.3 64.1 + - + +
1036C ARG* 3.0 27.3 + - - +
1037C ILE* 2.9 45.5 + - + +
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Residues in contact with GLN1034 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030C ILE* 3.3 25.6 + - - +
1031C MET* 3.0 13.4 + - + +
1033C GLN* 1.3 75.9 - - - +
1035C ASP* 1.3 67.7 + - - +
1037C ILE* 2.9 23.2 + - - +
1038C GLN* 3.0 37.7 + - - +
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Residues in contact with ASP1035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.3 29.3 + - - +
1031C MET* 2.9 24.9 + - - +
1032C ALA* 3.0 11.4 + - - +
1034C GLN* 1.3 77.7 - - - +
1036C ARG* 1.3 63.2 + - - +
1037C ILE 3.2 0.5 + - - -
1038C GLN* 4.9 8.0 + - - +
1039C GLN* 3.1 33.9 + - - +
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Residues in contact with ARG1036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 5.3 16.3 - - + +
19C ALA* 4.9 24.4 + - - +
38C MET* 4.9 10.7 - - - +
1029C ALA 4.7 2.0 + - - -
1032C ALA* 2.7 37.3 + - - +
1033C GLN* 3.4 32.6 - - - +
1035C ASP* 1.3 72.3 - - - +
1037C ILE* 1.3 64.4 + - + +
1039C GLN* 3.4 26.9 + - - +
1040C GLU* 3.6 11.3 - - - +
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Residues in contact with ILE1037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033C GLN* 2.9 40.6 + - + +
1034C GLN* 2.9 16.8 + - - +
1036C ARG* 1.3 77.1 - - + +
1038C GLN* 1.3 62.5 + - + +
1039C GLN 3.1 3.4 - - - -
1040C GLU* 2.9 16.0 + - - +
1041C ILE* 2.8 44.9 + - + +
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Residues in contact with GLN1038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034C GLN* 3.0 34.4 + - - +
1035C ASP* 4.9 7.4 + - - -
1037C ILE* 1.3 73.7 - - + +
1039C GLN* 1.3 60.5 + - - +
1041C ILE* 3.6 20.9 - - + +
1042C ALA* 3.2 21.7 + - - +
1086C ARG* 4.6 2.6 - - - -
1087C PRO 5.1 1.0 - - - +
1088C ASP* 3.5 32.1 - - + +
1212C CYS* 3.8 24.2 - - - +
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Residues in contact with GLN1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 5.1 11.7 - - - +
1035C ASP* 3.1 26.8 + - - +
1036C ARG* 3.4 22.9 + - - +
1037C ILE 3.0 0.8 + - - -
1038C GLN* 1.3 78.0 - - - +
1040C GLU* 1.3 65.6 + - + +
1042C ALA* 3.0 10.1 + - - +
1043C VAL* 2.9 22.0 + - - +
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Residues in contact with GLU1040 (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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1036C ARG 3.6 12.6 - - - +
1037C ILE* 2.9 21.6 + - - +
1039C GLN* 1.3 79.2 - - + +
1041C ILE* 1.3 74.6 + - + +
1042C ALA 3.0 1.1 - - - -
1043C VAL* 3.0 29.1 + - + +
1044C GLN* 3.0 29.6 + - - +
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Residues in contact with ILE1041 (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 ILE* 2.8 40.9 + - + +
1038C GLN* 3.6 14.6 - - + +
1040C GLU* 1.3 90.9 - - - +
1042C ALA* 1.3 58.6 + - - +
1044C GLN* 3.7 6.8 + - - +
1045C ASN* 3.0 30.9 + - - +
1086C ARG* 3.8 22.4 - - + -
1087C PRO* 3.9 31.6 - - + +
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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 GLN 3.2 17.2 + - - +
1039C GLN* 3.0 15.1 + - - +
1041C ILE* 1.3 76.0 - - - +
1043C VAL* 1.3 60.1 + - - +
1045C ASN 2.9 20.9 - - - +
1046C PRO* 4.9 0.3 - - - +
1086C ARG* 3.4 32.4 + - - +
1165C GLN* 6.0 1.3 - - - +
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Residues in contact with VAL1043 (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 GLN 2.9 9.6 + - - +
1040C GLU* 3.0 26.6 + - + +
1042C ALA* 1.3 81.8 - - - +
1044C GLN* 1.3 80.0 + - - +
1045C ASN 5.1 0.2 - - - -
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Residues in contact with GLN1044 (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 GLU* 3.0 30.7 + - - +
1041C ILE* 4.1 8.0 - - - +
1043C VAL* 1.3 100.1 - - + +
1045C ASN* 1.3 70.9 + - - +
1046C PRO* 4.0 5.9 - - - +
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Residues in contact with ASN1045 (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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1041C ILE* 3.0 13.7 + - - +
1042C ALA 2.9 21.2 - - - +
1043C VAL 5.1 0.2 - - - -
1044C GLN* 1.3 90.7 - - - +
1046C PRO* 1.3 73.9 - - + +
1084C LYS* 4.6 21.6 - - - +
1085C THR 4.5 6.7 + - - -
1086C ARG* 3.1 24.6 + - + -
1087C PRO* 4.0 20.8 - - + +
1265C HIS* 5.8 0.4 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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