Contacts of the helix formed by residues 1025 - 1045 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 4.7 6.0 - - + +
51A PHE* 3.6 33.3 - - + -
145A TYR 5.5 3.4 - - - +
146A ALA 4.1 15.5 - - - +
148A GLY 3.5 15.3 - - - +
149A GLY 2.8 1.4 + - - -
150A SER* 1.3 80.7 + - - +
1026A TYR* 1.3 65.2 + - - +
1027A ASP 3.0 1.0 + - - -
1028A GLU* 3.1 21.2 + - - +
1029A ALA 3.7 1.9 + - - -
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Residues in contact with TYR1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 2.9 31.4 + - - -
48A GLY* 5.4 0.2 - - - -
49A VAL* 4.3 19.5 - - + -
146A ALA 5.5 2.4 + - - -
147A MET* 3.8 35.4 - - + +
148A GLY 5.2 0.2 - - - -
149A GLY* 2.8 15.3 + - - +
150A SER 2.4 7.9 + - - -
1025A ALA* 1.3 71.5 - - - +
1027A ASP* 1.3 66.7 + - - +
1029A ALA* 2.9 10.4 + - + +
1030A ILE* 2.9 42.5 + - + +
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Residues in contact with ASP1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY 5.2 0.5 - - - +
150A SER* 2.6 25.8 + - - +
1026A TYR* 1.3 72.8 - - - +
1028A GLU* 1.3 52.1 + - - +
1030A ILE* 3.0 13.0 + - - +
1031A MET* 2.6 38.5 + - - +
90B ARG* 2.6 52.4 + - + +
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Residues in contact with GLU1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.8 18.5 + - - +
36A THR* 4.4 8.5 - - + +
51A PHE* 3.7 28.4 - - + -
1025A ALA* 3.1 12.6 + - - +
1027A ASP* 1.3 76.7 - - - +
1029A ALA* 1.3 53.2 + - - +
1031A MET* 3.1 12.6 + - + +
1032A ALA* 2.7 34.8 + - - +
66B LYS* 4.8 22.4 + - - +
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Residues in contact with ALA1029 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 5.2 6.1 - - - +
38A MET* 3.7 22.2 - - + +
49A VAL* 3.5 35.2 - - + -
51A PHE* 5.2 0.4 - - - -
1025A ALA 3.7 1.2 + - - -
1026A TYR* 2.9 12.2 + - + +
1028A GLU* 1.3 79.5 - - - +
1030A ILE* 1.3 59.1 + - + +
1032A ALA* 3.0 11.2 + - - +
1033A GLN* 2.9 26.6 + - - +
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Residues in contact with ILE1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A TYR* 2.9 40.5 + - + +
1027A ASP* 3.7 12.6 - - - +
1029A ALA* 1.3 76.5 - - + +
1031A MET* 1.3 61.5 + - - +
1033A GLN* 3.4 25.7 - - + +
1034A GLN* 3.3 25.7 - - - +
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Residues in contact with MET1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A ASP 2.6 20.6 + - - +
1028A GLU* 3.3 11.9 - - + +
1030A ILE* 1.3 72.6 - - - +
1032A ALA* 1.3 66.1 + - - +
1034A GLN* 3.0 14.9 + - + +
1035A ASP* 2.9 31.3 + - - +
63B LYS* 4.0 37.5 - - + +
64B PRO* 4.2 20.4 - - + -
90B ARG 6.0 1.6 - - - +
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Residues in contact with ALA1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 5.4 3.8 - - - +
36A THR* 4.7 13.9 - - + +
38A MET* 5.3 0.4 - - + -
1028A GLU 2.7 12.4 + - - +
1029A ALA* 3.2 13.9 - - - +
1031A MET* 1.3 78.2 - - - +
1033A GLN* 1.3 51.2 + - - +
1035A ASP* 3.0 12.3 + - - +
1036A ARG* 2.7 52.6 + - - +
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Residues in contact with GLN1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 5.9 2.9 - - + -
1029A ALA 2.9 13.0 + - - +
1030A ILE* 3.4 25.5 - - + +
1031A MET 3.1 0.2 - - - -
1032A ALA* 1.3 74.1 - - - +
1034A GLN* 1.3 64.8 + - + +
1036A ARG* 3.0 28.7 + - - +
1037A ILE* 2.9 45.8 + - + +
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Residues in contact with GLN1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A ILE* 3.3 24.7 + - - +
1031A MET* 3.2 12.3 - - + +
1033A GLN* 1.3 76.1 - - - +
1035A ASP* 1.3 65.1 + - - +
1037A ILE* 3.0 24.1 + - - +
1038A GLN* 3.0 36.1 + - - +
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Residues in contact with ASP1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031A MET* 2.9 26.0 + - - +
1032A ALA* 3.4 11.0 - - - +
1034A GLN* 1.3 78.2 - - - +
1036A ARG* 1.3 62.9 + - - +
1037A ILE 3.2 0.5 + - - -
1038A GLN* 4.9 8.4 + - - +
1039A GLN* 3.1 33.0 + - - +
63B LYS* 3.3 29.0 + - - +
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Residues in contact with ARG1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.9 28.3 - - + +
18A PRO 5.3 0.2 + - - -
19A ALA* 3.5 48.3 + - - +
22A SER* 4.8 9.7 + - - -
36A THR* 5.9 0.2 + - - -
38A MET* 4.1 16.0 - - - +
1032A ALA* 2.7 36.3 + - - +
1033A GLN* 3.4 32.3 + - - +
1035A ASP* 1.3 73.6 - - - +
1037A ILE* 1.3 64.6 + - + +
1039A GLN* 3.4 19.6 + - - +
1040A GLU* 3.6 11.6 - - - +
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Residues in contact with ILE1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A GLN* 2.9 40.6 + - + +
1034A GLN* 3.0 17.5 + - - +
1036A ARG* 1.3 77.2 - - + +
1038A GLN* 1.3 62.4 + - + +
1039A GLN 3.1 3.8 - - - -
1040A GLU* 2.9 16.4 + - - +
1041A ILE* 2.8 44.6 + - + +
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Residues in contact with GLN1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034A GLN* 3.0 34.8 + - - +
1035A ASP* 4.9 7.1 + - - +
1037A ILE* 1.3 75.1 - - + +
1039A GLN* 1.3 58.6 + - - +
1041A ILE* 3.6 20.9 - - + +
1042A ALA* 3.2 22.3 + - - +
1086A ARG* 4.6 2.4 - - - -
1087A PRO 5.1 1.4 - - - +
1088A ASP* 3.5 32.8 - - + +
1212A CYS* 3.8 23.7 - - - +
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Residues in contact with GLN1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA* 4.7 6.5 + - - +
17A PRO* 3.3 33.9 - - - +
1035A ASP* 3.1 26.6 + - - +
1036A ARG* 3.4 14.9 + - - +
1037A ILE 3.1 0.6 - - - -
1038A GLN* 1.3 77.9 - - - +
1040A GLU* 1.3 64.6 + - + +
1042A ALA* 3.0 9.6 + - - +
1043A VAL* 2.9 22.7 + - - +
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Residues in contact with GLU1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 5.9 4.5 - - + -
1036A ARG 3.6 12.8 - - - +
1037A ILE* 2.9 22.0 + - - +
1039A GLN* 1.3 79.7 - - + +
1041A ILE* 1.3 73.1 + - + +
1042A ALA 3.0 1.6 - - - -
1043A VAL* 3.0 31.1 + - + +
1044A GLN* 3.0 29.9 + - - +
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Residues in contact with ILE1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037A ILE* 2.8 38.5 + - + +
1038A GLN* 3.6 15.0 - - + +
1040A GLU* 1.3 92.4 - - + +
1042A ALA* 1.3 58.7 + - - +
1044A GLN* 3.7 7.1 + - - +
1045A ASN* 3.0 31.0 + - - +
1086A ARG* 3.8 21.5 - - + -
1087A PRO* 3.9 31.0 - - + +
1088A ASP* 5.3 0.2 - - - -
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Residues in contact with ALA1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038A GLN 3.2 17.1 + - - +
1039A GLN* 3.0 13.9 + - - +
1041A ILE* 1.3 76.9 - - - +
1043A VAL* 1.3 60.6 + - - +
1045A ASN 2.9 21.0 - - - +
1046A PRO* 4.9 0.7 - - - +
1086A ARG* 3.4 33.4 + - - +
1165A GLN* 6.0 1.1 - - - +
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Residues in contact with VAL1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039A GLN 2.9 9.8 + - - +
1040A GLU* 3.0 26.5 + - + +
1042A ALA* 1.3 81.2 - - - +
1044A GLN* 1.3 79.5 + - - +
1045A ASN 5.1 0.3 - - - -
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Residues in contact with GLN1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A GLU* 3.0 30.8 + - - +
1041A ILE* 4.1 6.9 - - - +
1043A VAL* 1.3 99.1 - - - +
1045A ASN* 1.3 71.8 + - - +
1046A PRO* 4.0 5.4 - - - +
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Residues in contact with ASN1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041A ILE* 3.0 13.7 + - - +
1042A ALA 2.9 20.6 - - - +
1043A VAL 5.0 0.2 - - - -
1044A GLN* 1.3 89.2 - - - +
1046A PRO* 1.3 75.7 - - + +
1084A LYS* 4.6 22.0 - - - +
1085A THR 4.5 6.7 + - - -
1086A ARG* 3.1 24.4 + - + -
1087A PRO* 4.0 21.6 - - + +
1265A HIS* 5.8 0.2 + - - -
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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