Contacts of the helix formed by residues 91 - 100 (chain I) in PDB entry 1JJ2
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 LYS 91 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6150 G 3.2 31.7 + - - +
6160 U 4.0 21.0 + - - -
11050 C 4.5 12.1 + - - -
88I PRO* 3.0 24.0 + - + +
90I LYS* 1.3 82.6 - - - +
92I GLN* 1.3 59.9 + - - +
93I ARG* 4.4 13.7 - - + +
94I GLY 3.2 6.0 + - - +
95I ARG* 2.8 28.7 + - - +
8502I CL 3.7 8.0 - - + +
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Residues in contact with GLN 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6130 C 4.4 15.0 + - - -
6140 U 4.1 34.6 + - - +
90I LYS 4.1 0.4 + - - -
91I LYS* 1.3 73.9 - - - +
93I ARG* 1.3 68.9 + - - +
95I ARG* 3.2 4.9 + - - +
96I GLU* 2.9 47.3 + - - +
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Residues in contact with ARG 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6150 G 5.0 5.4 + - - +
11040 C 5.6 1.4 + - - -
11050 C 3.4 28.1 + - - -
11060 A 5.6 1.8 + - - -
31I LEU* 4.2 36.4 + - + +
88I PRO* 4.1 18.4 - - - +
91I LYS* 3.4 14.9 - - + +
92I GLN* 1.3 82.9 + - - +
94I GLY* 1.3 60.9 + - - +
96I GLU* 3.3 13.3 + - - +
97I ALA* 3.0 22.3 + - - +
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Residues in contact with GLY 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LEU* 4.5 5.6 - - - -
87I LEU* 4.2 3.0 - - - +
88I PRO* 3.0 40.0 + - - +
89I HIS* 3.9 5.0 - - - -
91I LYS 3.2 4.4 + - - -
93I ARG* 1.3 82.4 - - - +
95I ARG* 1.3 60.5 + - - +
97I ALA* 3.4 2.6 + - - +
98I PHE* 3.0 24.8 + - - +
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Residues in contact with ARG 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5330 U 2.8 59.0 + - - -
5340 C 4.0 11.9 + - - -
28140 A 3.1 33.7 + - - -
89I HIS* 3.5 22.4 + - - +
90I LYS 5.4 0.4 - - - -
91I LYS 2.8 18.5 + - - +
92I GLN* 3.8 4.5 - - - +
94I GLY* 1.3 72.3 - - - +
96I GLU* 1.3 59.0 + - - +
98I PHE* 3.8 8.1 - - + +
99I GLU* 2.7 53.7 + - + +
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I GLN* 2.9 43.8 + - + +
93I ARG* 3.5 10.5 - - - +
95I ARG* 1.3 76.7 - - - +
97I ALA* 1.3 61.9 + - - +
99I GLU* 3.3 9.7 + - - +
100I SER* 3.2 22.1 + - - -
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Residues in contact with ALA 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ALA* 3.4 35.8 - - + +
31I LEU* 3.7 17.5 - - + +
87I LEU* 4.3 4.7 - - + -
93I ARG 3.0 15.9 + - - +
94I GLY 3.7 4.5 - - - +
96I GLU* 1.3 77.0 - - - +
98I PHE* 1.3 59.0 + - - +
100I SER* 2.7 31.8 + - - -
101I VAL* 3.5 10.0 + - - +
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Residues in contact with PHE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28150 G 5.5 4.5 - - - -
80I LYS* 3.4 48.7 - - + -
81I ARG* 5.5 0.7 - - - -
83I ILE* 4.7 5.8 - - + -
84I ARG* 3.4 55.9 - - + -
87I LEU* 3.5 17.2 - - + +
89I HIS* 4.8 7.6 - - + -
94I GLY 3.0 18.3 + - - +
95I ARG* 3.8 9.2 - - + +
97I ALA* 1.3 77.2 - - - +
99I GLU* 1.3 69.7 + - + +
101I VAL* 3.3 23.4 + - + +
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Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28140 A 3.0 16.1 + - - -
28150 G 3.0 36.6 + - - +
6I PHE* 4.5 9.5 - - - -
80I LYS* 5.4 1.3 - - - +
95I ARG* 2.7 56.6 + - + +
96I GLU* 3.8 7.1 - - - +
97I ALA 3.1 0.2 - - - -
98I PHE* 1.3 83.8 - - + +
100I SER* 1.3 57.5 + - - +
101I VAL 3.2 6.2 + - - +
102I ARG* 4.8 6.1 + - - +
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Residues in contact with SER 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I PHE* 3.8 10.8 - - - -
30I ALA* 4.4 1.9 + - - +
33I GLY 5.6 1.1 + - - -
34I GLU 3.7 12.5 + - - -
35I THR* 3.3 21.0 - - - +
36I VAL 3.0 24.1 + - - +
96I GLU 3.2 11.7 + - - -
97I ALA* 2.7 25.7 + - - -
99I GLU* 1.3 77.3 - - - +
101I VAL* 1.3 58.5 + - - +
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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