Contacts of the helix formed by residues 93 - 103 (chain d) in PDB entry 5JPQ
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 SER 93 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91d ILE 3.7 0.4 + - - -
92d THR* 1.3 73.4 - - - +
94d CYS* 1.3 58.5 + - - +
96d MET* 3.3 4.4 + - - +
97d ALA* 2.9 31.2 + - - +
120d ARG* 6.1 3.4 - - - -
121d LEU 3.4 13.2 + - - -
122d THR* 5.1 3.4 - - - -
123d CYS* 4.8 13.5 - - - +
126d LYS* 3.8 16.1 - - - +
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Residues in contact with CYS 94 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92d THR* 3.3 2.9 - - - -
93d SER* 1.3 76.7 - - - +
95d VAL* 1.3 64.8 + - - +
97d ALA* 3.7 2.1 - - - +
98d GLU* 3.1 23.7 + - - +
123d CYS* 5.6 1.7 - - + +
125d HIS 4.1 0.2 - - - +
126d LYS* 3.0 40.0 - - - +
128d THR 3.5 19.7 - - - +
130d ALA* 4.7 4.9 + - - -
133d CYS* 3.6 20.4 - - + -
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Residues in contact with VAL 95 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60d VAL 4.4 10.5 - - - +
61d ASP* 4.5 3.8 - - + -
62d THR* 3.6 29.5 - - - +
91d ILE* 4.9 3.4 - - + -
92d THR* 3.2 22.8 + - - +
94d CYS* 1.3 81.2 - - - +
96d MET* 1.3 58.4 + - - +
98d GLU* 3.4 3.7 + - - +
99d LEU* 3.0 22.2 + - - +
130d ALA* 4.5 17.8 - - + +
133d CYS* 5.4 0.4 - - + +
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Residues in contact with MET 96 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91d ILE* 5.0 10.5 - - + +
92d THR 3.1 16.5 + - - +
93d SER* 4.1 4.7 - - - +
95d VAL* 1.3 75.3 - - - +
97d ALA* 1.3 60.2 + - - +
99d LEU* 3.3 10.0 - - - +
100d GLU* 2.8 25.5 + - - +
113d ALA* 5.2 16.2 - - + +
114d ARG* 6.3 0.7 - - - -
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Residues in contact with ALA 97 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93d SER 2.9 19.1 + - - +
94d CYS* 3.7 7.6 - - - +
96d MET* 1.3 73.5 - - - +
98d GLU* 1.3 57.9 + - - +
100d GLU* 2.6 35.6 + - - +
101d LYS* 3.0 5.9 + - - +
126d LYS* 4.7 10.1 - - + +
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Residues in contact with GLU 98 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62d THR* 4.6 9.4 - - - -
94d CYS 3.1 11.3 + - - +
95d VAL* 3.4 11.4 - - - +
97d ALA* 1.3 77.9 - - - +
99d LEU* 1.3 62.1 + - - +
101d LYS* 3.1 15.6 + - - +
102d LEU* 3.1 11.8 + - - +
130d ALA* 5.0 10.1 - - + +
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Residues in contact with LEU 99 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62d THR* 4.6 11.1 - - - +
65d LEU* 6.2 2.5 - - + -
95d VAL 3.0 15.3 + - - +
96d MET* 3.3 13.0 - - + +
97d ALA 3.2 0.2 - - - -
98d GLU* 1.3 73.7 - - - +
100d GLU* 1.3 53.2 + - - +
102d LEU* 2.8 12.2 + - + +
103d GLY* 2.6 34.9 + - - -
109d ALA* 5.4 6.0 - - + +
110d LEU* 5.0 14.5 + - + +
113d ALA* 5.0 14.1 - - + -
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Residues in contact with GLU 100 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96d MET 2.8 12.7 + - - +
97d ALA* 2.6 24.0 + - - +
99d LEU* 1.3 70.8 - - - +
101d LYS* 1.3 59.8 + - - +
103d GLY* 3.2 11.8 + - - +
104d PRO* 3.6 6.8 - - - +
110d LEU* 5.5 7.0 - - - -
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Residues in contact with LYS 101 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97d ALA 3.0 8.8 + - - +
98d GLU* 3.1 9.8 + - - +
100d GLU* 1.3 73.5 - - - +
102d LEU* 1.3 66.3 + - - +
104d PRO* 3.0 17.2 - - - +
105d ARG 4.5 0.5 + - - -
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Residues in contact with LEU 102 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66d SER* 6.5 1.3 - - - -
98d GLU 3.1 7.6 + - - +
99d LEU* 2.8 16.5 + - - +
101d LYS* 1.3 76.4 - - - +
103d GLY* 1.3 62.2 + - - +
104d PRO 3.1 1.6 - - - -
105d ARG* 3.2 4.2 + - - +
106d TYR* 3.2 28.2 + - + +
109d ALA* 6.1 5.2 - - + -
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Residues in contact with GLY 103 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99d LEU 2.6 17.8 + - - -
100d GLU* 3.6 6.5 - - - -
101d LYS 3.0 1.0 - - - -
102d LEU* 1.3 71.0 - - - +
104d PRO* 1.3 65.0 - - - +
105d ARG 3.1 1.3 + - - -
106d TYR 3.8 15.9 + - - -
107d ARG* 4.2 12.1 + - - +
109d ALA* 6.4 0.9 - - - -
110d LEU* 5.1 13.2 - - - -
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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
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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