Contacts of the strand formed by residues 77 - 82 (chain D) in PDB entry 2JIX
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 GLN 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D THR* 3.9 15.3 + - - +
22D CYS 3.0 16.6 - - - +
23D THR* 3.1 32.0 - - - +
24D VAL* 4.6 1.6 - - - +
29D ILE* 3.8 11.1 - - - +
72D ASP* 2.9 33.3 + - + +
75D LYS* 3.8 41.6 - - + +
76D ASN* 1.3 79.1 - - - +
78D PHE* 1.3 61.9 + - - +
79D SER* 5.4 0.9 - - - -
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D THR* 3.7 2.1 - - - -
22D CYS* 2.9 47.5 + - - +
24D VAL* 4.3 8.3 - - + -
29D ILE* 5.3 1.6 - - + -
34D TRP* 3.2 51.8 - + + -
35D SER 3.8 17.5 - - - -
36D TRP* 3.3 40.2 - + - -
51D ILE* 3.9 15.0 - - + -
69D ILE* 4.3 0.7 - - + -
70D SER 3.1 15.5 - - - +
71D VAL* 3.5 18.6 - - + +
77D GLN* 1.3 74.6 - - - +
79D SER* 1.3 62.8 + - - +
95D CYS* 3.9 12.6 - - + -
96D ALA 3.9 2.5 - - - -
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU 2.8 18.5 + - - -
21D THR* 3.4 18.0 - - - +
36D TRP* 3.5 6.7 - - - +
68D THR 3.9 0.3 - - - +
69D ILE* 3.3 10.0 - - - +
70D SER* 3.0 43.5 + - - -
77D GLN 5.4 0.4 - - - -
78D PHE* 1.3 76.5 - - - +
80D LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 80 (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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18D LEU* 3.8 5.1 - - + +
19D SER* 3.5 4.0 - - - -
20D LEU* 3.0 42.4 + - + +
36D TRP* 3.4 39.2 - - + +
48D ILE* 3.3 31.0 - - + -
67D VAL* 4.2 14.1 - - + -
68D THR 3.7 2.9 - - - +
69D ILE* 4.7 2.5 - - + -
79D SER* 1.3 73.1 + - - +
81D LYS* 1.3 78.0 + - - +
82D LEU* 4.3 10.5 - - + +
93D TYR* 3.6 33.2 - - + -
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 5.0 10.0 + - - +
18D LEU 3.4 2.5 - - - +
19D SER* 3.5 25.4 - - - +
66D ARG 3.6 4.7 - - - +
67D VAL* 3.8 1.6 - - - -
68D THR* 2.9 55.6 + - + +
80D LEU* 1.3 74.2 - - - +
82D LEU* 1.3 61.8 + - - +
83D ARG* 3.3 29.8 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 4.4 1.1 - - - -
18D LEU* 2.9 47.3 + - + +
38D ARG* 5.7 0.4 - - - +
48D ILE* 5.7 1.3 - - + -
63D LEU* 3.7 29.2 - - + -
66D ARG* 3.2 48.7 - - + +
67D VAL* 4.0 9.4 - - + -
80D LEU* 4.2 14.6 - - + -
81D LYS* 1.3 71.8 - - - +
83D ARG* 1.3 62.1 + - - +
85D VAL* 3.1 27.3 - - + +
89D ASP* 4.0 11.2 - - + +
93D TYR* 4.9 9.4 - - + +
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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
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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