Contacts of the helix formed by residues 1012 - 1032 (chain C) in PDB entry 2NB1
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 GLY1012 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASP* 5.0 6.2 + - - -
6A LEU* 5.2 3.7 - - - +
1010C VAL* 4.2 2.0 - - - +
1011C ARG* 1.3 72.8 - - - +
1013C ARG* 1.3 62.0 + - - +
1014C GLU 3.6 1.1 - - - -
1015C THR* 3.4 23.6 - - - -
1016C TYR* 2.9 31.1 + - - +
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Residues in contact with ARG1013 (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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1A SER 2.7 33.3 + - - +
2A ASP* 3.7 21.7 + - - +
4A GLU* 3.9 22.2 + - - +
6A LEU* 6.4 2.0 - - - -
1012C GLY* 1.3 71.8 - - - +
1014C GLU* 1.3 63.9 + - - +
1016C TYR* 3.4 3.0 + - - +
1017C GLU* 3.2 37.4 + - - +
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Residues in contact with GLU1014 (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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107B LYS* 6.1 4.5 - - - +
111B ILE* 6.0 1.2 - - - +
114B LYS* 4.5 21.4 + - - +
1013C ARG* 1.3 76.1 - - - +
1015C THR* 1.3 59.7 + - - +
1017C GLU* 4.2 15.0 - - + +
1018C MET* 2.9 48.5 + - + +
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Residues in contact with THR1015 (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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23A LYS* 3.6 38.6 - - + +
30A GLN* 5.5 5.2 + - - +
1010C VAL* 4.2 7.0 - - + -
1012C GLY* 3.4 24.3 - - - -
1013C ARG 3.2 0.2 - - - -
1014C GLU* 1.3 77.8 + - - +
1016C TYR* 1.3 60.1 + - - +
1018C MET* 5.0 0.7 - - - -
1019C LEU* 3.2 38.9 + - + +
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Residues in contact with TYR1016 (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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6A LEU* 3.6 42.7 - - + +
7A TYR 2.8 29.4 + - - -
8A LEU* 3.8 29.8 - - + +
9A PRO* 5.0 2.3 - - - +
1010C VAL* 5.0 14.3 - - + +
1012C GLY 2.9 19.3 + - - +
1013C ARG* 3.9 3.8 - - - +
1014C GLU 3.3 0.2 - - - -
1015C THR* 1.3 77.1 - - - +
1017C GLU* 1.3 58.8 + - + +
1019C LEU* 3.8 2.0 - - - +
1020C LEU* 2.8 59.3 + - + +
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Residues in contact with GLU1017 (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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1013C ARG* 3.2 26.5 + - - +
1014C GLU* 3.8 14.6 - - + +
1016C TYR* 1.3 79.5 - - + +
1018C MET* 1.3 59.1 + - - +
1020C LEU* 3.7 3.6 - - - +
1021C GLU* 2.8 36.2 + - - +
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Residues in contact with MET1018 (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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26A LEU* 6.0 1.1 - - + -
111B ILE* 3.7 40.6 - - + -
114B LYS* 3.9 28.3 - - + -
115B LEU* 4.1 21.3 - - + -
1014C GLU* 2.9 33.6 + - + +
1015C THR* 5.0 0.9 - - - -
1017C GLU* 1.3 73.6 - - - +
1019C LEU* 1.3 80.3 + - + +
1021C GLU* 4.1 4.7 - - - +
1022C ILE* 3.2 54.5 + - + +
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Residues in contact with LEU1019 (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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8A LEU* 4.5 16.4 - - + -
19A LEU* 3.7 29.7 - - + +
22A ILE* 5.9 4.7 - - + -
23A LYS* 4.2 34.5 - - + +
115B LEU* 5.9 2.9 - - + -
1008C LEU* 6.5 0.4 - - + -
1015C THR* 3.2 34.0 + - + +
1016C TYR 4.0 1.1 - - - +
1018C MET* 1.3 98.5 - - + +
1020C LEU* 1.3 57.2 + - - +
1022C ILE* 4.3 3.3 - - - +
1023C LYS* 2.9 30.5 + - - +
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Residues in contact with LEU1020 (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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8A LEU* 4.5 16.3 - - + +
1016C TYR* 2.8 49.2 + - + +
1017C GLU* 3.8 3.6 - - - +
1019C LEU* 1.3 73.9 - - - +
1021C GLU* 1.3 56.8 + - - +
1023C LYS* 3.1 8.4 + - + -
1024C GLU* 2.8 59.8 + - + +
1134D ARG* 4.8 15.7 - - - +
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Residues in contact with GLU1021 (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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107B LYS* 5.3 11.8 - - - +
1017C GLU* 2.8 23.4 + - - +
1018C MET* 4.1 5.2 - - - +
1020C LEU* 1.3 70.8 - - - +
1022C ILE* 1.3 56.2 + - + +
1024C GLU* 3.9 4.8 - - - +
1025C SER* 2.7 39.0 + - - +
1119D LEU* 3.7 25.3 - - + +
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Residues in contact with ILE1022 (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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111B ILE* 3.6 25.1 - - + -
112B LEU* 6.2 0.2 - - + -
115B LEU* 4.8 5.8 - - + -
1018C MET* 3.2 46.5 + - + +
1019C LEU* 4.3 2.9 - - + +
1021C GLU* 1.3 74.6 - - + +
1023C LYS* 1.3 60.8 + - - +
1025C SER* 3.4 1.4 + - - -
1026C LEU* 2.9 32.2 + - - +
1115D LEU* 3.5 41.7 - - + -
1118D SER* 4.0 0.9 + - - +
1119D LEU* 3.9 25.6 - - + -
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Residues in contact with LYS1023 (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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8A LEU* 4.7 12.1 - - + -
10A VAL* 3.2 44.0 - - + -
15A THR* 3.7 22.1 - - + +
19A LEU* 4.1 24.7 - - + +
1019C LEU 2.9 22.7 + - - +
1020C LEU* 3.5 9.0 - - + +
1022C ILE* 1.3 77.2 - - - +
1024C GLU* 1.3 56.2 + - - +
1026C LEU* 3.8 5.3 - - + +
1027C GLU* 2.8 79.5 + - - +
1030C GLN* 5.4 1.0 + - - -
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Residues in contact with GLU1024 (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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1020C LEU* 2.8 38.6 + - + +
1021C GLU* 3.9 4.5 - - - +
1023C LYS* 1.3 71.1 - - - +
1025C SER* 1.3 59.3 + - - +
1026C LEU 3.2 0.2 + - - -
1027C GLU* 3.2 5.1 + - - +
1028C LEU* 2.8 51.2 + - + +
1122D MET* 4.5 4.4 - - + +
1130D VAL* 3.7 26.1 - - + +
1133D TYR* 5.8 2.8 - - - -
1134D ARG* 4.6 22.4 + - - +
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Residues in contact with SER1025 (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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1021C GLU* 2.7 25.5 + - - +
1022C ILE 3.7 2.5 - - - -
1024C GLU* 1.3 75.5 - - - +
1026C LEU* 1.3 57.6 + - - +
1028C LEU* 3.9 1.4 - - - +
1029C MET* 3.0 29.8 + - - +
1118D SER* 3.1 16.5 + - - +
1119D LEU* 3.7 21.3 - - - +
1122D MET* 3.5 43.8 - - - +
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Residues in contact with LEU1026 (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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15A THR* 5.6 7.2 - - + +
18A MET* 5.6 3.6 - - + -
1022C ILE 2.9 16.7 + - - +
1023C LYS* 3.8 5.8 - - + +
1025C SER* 1.3 73.3 - - - +
1027C GLU* 1.3 63.9 + - - +
1029C MET* 3.1 28.6 + - + +
1030C GLN* 3.0 50.5 + - + +
1114D LYS* 4.1 24.7 - - + +
1115D LEU* 4.1 19.3 - - + -
1118D SER* 2.9 16.0 + - - +
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Residues in contact with GLU1027 (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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10A VAL* 4.6 5.9 - - - +
11A ARG* 3.5 24.8 + - - +
15A THR* 5.4 1.2 + - - +
1023C LYS* 2.8 49.3 + - - +
1024C GLU* 3.8 3.6 - - - +
1026C LEU* 1.3 73.0 - - - +
1028C LEU* 1.3 59.8 + - + +
1030C GLN* 3.1 22.5 - - + +
1031C TYR* 2.9 36.1 + - + +
1133D TYR* 2.8 33.6 + - + -
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Residues in contact with LEU1028 (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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1024C GLU* 2.8 40.1 + - + +
1025C SER 4.0 2.7 - - - +
1027C GLU* 1.3 74.7 - - + +
1029C MET* 1.3 58.7 + - - +
1031C TYR* 4.2 8.7 - - + -
1032C LEU* 2.9 47.1 + - + +
1122D MET* 4.5 6.3 - - - -
1129D LEU* 3.7 19.1 - - + +
1130D VAL* 3.6 49.1 - - + +
1133D TYR* 3.5 34.5 - - + -
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Residues in contact with MET1029 (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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1025C SER 3.0 19.8 + - - +
1026C LEU* 3.1 20.2 + - + +
1028C LEU* 1.3 75.8 - - - +
1030C GLN* 1.3 58.6 + - + +
1031C TYR 3.7 0.2 + - - -
1032C LEU 3.9 3.5 - - - +
1034C GLN* 3.3 31.3 - - + +
1037C ILE* 3.8 33.9 - - + -
1114D LYS* 3.8 8.7 - - + +
1117D GLU* 4.5 6.7 - - + +
1118D SER* 3.5 42.4 - - - +
1121D LEU* 4.6 5.4 - - - -
1122D MET* 6.3 0.9 - - + +
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Residues in contact with GLN1030 (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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15A THR* 4.3 15.1 + - - +
1023C LYS* 5.4 0.5 + - - -
1026C LEU* 3.0 37.2 + - + +
1027C GLU* 3.1 28.7 - - + +
1029C MET* 1.3 75.3 - - + +
1031C TYR* 1.3 59.5 + - + +
1032C LEU 4.7 1.1 - - - -
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Residues in contact with TYR1031 (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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1027C GLU* 2.9 22.1 + - + +
1028C LEU* 3.9 10.1 - - + +
1030C GLN* 1.3 79.1 - - + +
1032C LEU* 1.3 67.2 + - - +
1033C PRO* 4.0 1.0 - - - +
1129D LEU* 4.2 20.3 - - + +
1133D TYR* 3.8 49.4 - + + +
1136D GLN* 4.8 9.0 + - - -
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Residues in contact with LEU1032 (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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1028C LEU* 2.9 38.5 + - + +
1029C MET 3.9 4.5 - - - +
1030C GLN 4.7 0.7 - - - -
1031C TYR* 1.3 78.0 - - - +
1033C PRO* 1.3 75.4 - - + +
1034C GLN* 2.8 56.6 + - - +
1122D MET* 5.8 1.3 - - - -
1125D VAL* 5.6 0.7 - - + -
1126D PRO 5.2 7.9 - - - +
1128D PRO* 5.6 7.0 - - + -
1129D LEU* 3.5 39.7 - - + +
1130D VAL* 4.7 8.1 - - + -
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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