Contacts of the strand formed by residues 78 - 81 (chain B) in PDB entry 2IGT
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.6 6.6 - - - -
69B THR 3.3 13.9 - - - -
70B GLY* 4.5 4.7 - - - -
77B MSE 1.3 77.0 - - - +
79B ARG* 1.3 60.7 + - - -
106B ALA* 2.7 20.5 + - - +
222C GLU* 3.7 5.9 - - - -
223C VAL* 2.9 31.3 + - - -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 4.0 3.0 - - - -
69B THR* 2.7 46.6 + - - +
70B GLY* 5.1 0.4 - - - -
78B GLY* 1.3 75.2 - - - +
80B TRP* 1.3 77.8 + - - +
106B ALA* 5.9 0.7 - - - +
-2C PHE* 3.9 7.2 - - + -
190C ASP* 2.7 44.3 + - - -
192C MSE 3.5 27.6 - - - +
222C GLU* 3.6 19.3 + - + +
223C VAL 2.8 37.7 + - - +
224C TRP* 3.7 15.8 - - - +
229C HIS* 3.7 19.3 + - + +
1018C FMT 2.8 29.0 + - - +
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 4.4 5.6 - - + -
44B VAL 4.1 2.9 - - - -
45B ARG* 3.8 19.5 - - + -
66B ALA* 3.7 29.4 - - + -
67B ILE 3.4 11.0 - - - -
68B PHE* 3.4 47.5 - + + -
79B ARG* 1.3 86.0 - - - +
81B ARG* 1.3 58.6 + - - +
82B PHE* 3.6 29.9 + - + -
104B PHE* 3.6 29.6 - + + -
105B THR 3.0 34.1 + - - +
107B PHE 3.4 11.0 + - - -
108B ARG 4.0 16.4 - - - -
109B HIS 4.9 1.6 - - - -
110B VAL* 4.0 14.4 - - + -
-2C PHE* 5.1 0.2 - - - -
222C GLU* 6.2 0.8 - - - +
1018C FMT 4.3 9.0 - - - +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.2 6.2 - - - -
67B ILE* 2.8 46.3 + - + +
69B THR* 4.2 6.7 - - + -
79B ARG 3.7 1.0 + - - -
80B TRP* 1.3 72.9 - - - +
82B PHE* 1.3 77.9 + - - +
83B PRO* 3.4 25.6 + - + +
-3C TYR* 2.7 32.9 + - + +
-2C PHE* 3.6 31.2 - - + -
-1C GLN 5.0 5.5 + - - -
196C GLN* 3.6 6.9 + - - +
232C LEU* 3.6 33.8 - - - +
1004C GOL 2.9 32.7 + - - -
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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