Contacts of the strand formed by residues 145 - 151 (chain P) in PDB entry 2D2C
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 GLY 145 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N MET* 5.4 8.1 - - - -
80N TRP* 6.5 0.4 - - - -
59O PRO* 3.5 24.0 - - - -
60O ALA 4.9 0.9 - - - -
144P PHE* 1.3 80.2 - - - +
146P LYS* 1.3 65.1 + - - -
247P ILE 3.8 2.1 - - - +
248P VAL* 4.1 4.0 - - - -
249P LEU* 2.8 29.2 + - - +
250P GLN* 6.0 0.4 - - - +
254P ARG* 5.6 1.2 - - - +
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Residues in contact with LYS 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N ARG* 2.9 26.8 - - - +
58O ASP* 3.1 22.5 + - - +
59O PRO* 2.7 36.3 + - + +
60O ALA 3.4 17.1 + - - +
61O MET* 4.4 2.7 - - - -
62O VAL* 3.4 16.3 - - - +
1309O BNT 3.8 19.1 - - + -
144P PHE 4.2 0.3 - - - +
145P GLY* 1.3 76.6 - - - -
147P TYR* 1.3 67.9 + - - +
246P GLU* 3.6 29.2 - - + +
247P ILE 3.5 6.5 - - - +
248P VAL* 3.3 21.1 - - + -
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Residues in contact with TYR 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ASN* 4.9 4.6 + - - -
62O VAL* 4.6 13.5 - - + -
1309O BNT 3.5 6.1 - - + -
77P MET* 6.1 2.0 - - + -
79P PRO* 3.4 31.0 - - + -
80P GLU* 4.2 29.9 + - + +
82P PHE* 6.0 0.9 - + - -
142P ILE* 5.3 1.1 - - + +
143P HIS* 3.3 39.1 + - + +
144P PHE 2.7 30.7 - - - -
145P GLY 3.6 3.6 - - - -
146P LYS* 1.3 86.0 - - - +
148P ALA* 1.3 63.9 + - - +
149P ILE* 3.9 1.6 - - - +
246P GLU* 3.0 23.4 - - - -
247P ILE* 3.2 14.4 + - + +
249P LEU* 4.0 8.7 - - + -
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Residues in contact with ALA 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309O BNT 2.7 38.9 - - + +
77P MET* 3.2 24.0 - - + +
79P PRO* 3.9 10.0 - - - +
147P TYR* 1.3 76.2 - - - +
149P ILE* 1.3 62.9 + - - +
150P HIS* 3.0 31.0 - - + +
245P THR 3.5 7.6 - - - +
246P GLU* 4.3 0.7 - - - -
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Residues in contact with ILE 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P VAL* 5.4 4.9 - - + +
36P VAL* 4.2 19.3 - - + -
76P LEU* 4.2 19.1 - - + -
77P MET 3.1 15.7 - - - +
78P LEU* 4.7 6.1 - - + -
79P PRO* 4.1 14.8 - - + -
147P TYR 3.9 4.0 - - - +
148P ALA* 1.3 82.4 - - - +
150P HIS* 1.3 63.5 + - - +
151P LEU* 6.1 0.2 - - + -
244P ASP* 3.3 1.2 - - - -
245P THR* 2.6 54.8 + - + +
246P GLU* 4.0 4.5 - - - -
247P ILE* 3.8 38.4 - - + +
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Residues in contact with HIS 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O GLU* 4.6 8.0 + - - -
1309O BNT 5.1 7.7 - + + -
14P ARG* 2.8 51.0 + - + +
20P ILE* 5.3 4.5 - - + -
34P VAL* 5.7 0.2 - - - -
76P LEU* 3.5 3.3 - - - +
77P MET* 2.8 56.2 + - + +
148P ALA* 3.0 29.5 - - + +
149P ILE* 1.3 98.1 - - - +
151P LEU* 1.3 62.9 + - - +
243P ASP 3.9 1.3 - - - -
244P ASP* 3.6 27.1 - - + +
245P THR 4.4 1.3 + - - -
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ILE* 4.5 6.2 - - - +
32P ALA* 4.5 10.8 - - + -
33P GLU 4.8 0.7 - - - +
34P VAL* 3.1 39.0 - - + -
50P VAL* 3.3 22.9 - - + -
74P ALA* 4.5 8.5 - - + -
75P VAL* 3.5 18.6 - - - +
76P LEU* 4.2 13.9 - - + +
129P PHE* 6.0 0.7 - - + -
149P ILE* 6.1 0.2 - - + -
150P HIS* 1.3 78.9 - - - +
152P GLY* 1.3 64.3 + - - +
153P ALA* 3.8 17.7 - - + +
242P GLN* 3.2 26.1 - - - +
243P ASP* 3.2 19.5 + - + +
244P ASP* 4.2 1.2 + - - -
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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