Contacts of the strand formed by residues 102 - 108 (chain B) in PDB entry 3T30
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 VAL 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B TRP 3.8 0.9 - - - +
31B THR* 3.3 2.6 - - - -
32B PHE* 2.8 50.8 + - + +
44B LEU* 3.8 27.4 - - + -
64B ILE* 3.8 23.1 - - + -
65B LEU 5.5 0.4 - - - -
98B LEU* 4.0 22.2 - - + -
99B SER 4.5 4.7 - - - +
100B PRO* 4.5 3.6 - - + -
101B PRO* 1.3 76.8 - - - +
103B THR* 1.3 64.4 + - - +
104B PHE* 3.8 26.0 + - + -
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Residues in contact with THR 103 (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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29B THR* 4.5 9.0 - - - -
30B TRP 3.4 4.9 - - - +
31B THR* 2.8 27.6 + - - +
33B ARG* 5.2 3.1 + - - -
64B ILE* 3.3 5.5 - - - +
65B LEU* 2.8 67.5 + - + -
66B PRO 5.4 2.0 + - - -
67B PRO 6.3 0.2 - - - -
101B PRO* 5.6 1.4 - - - +
102B VAL* 1.3 76.5 - - - +
104B PHE* 1.3 72.6 + - - +
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Residues in contact with PHE 104 (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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19B TRP* 3.6 24.7 - + - -
21B CYS* 4.5 1.8 - - - -
23B LEU* 4.1 20.4 - - + +
28B ARG 4.4 0.2 - - - -
29B THR* 3.2 6.6 - - - -
30B TRP* 2.8 56.5 + + - +
44B LEU* 3.8 24.0 - - + -
46B LEU* 4.3 5.8 - - + -
62B VAL* 4.5 2.2 - - + -
63B GLU 3.4 4.5 - - - +
64B ILE* 3.9 21.3 - - + -
80B ILE* 3.8 20.4 - - + -
98B LEU* 3.9 9.6 - - + -
102B VAL* 3.8 15.5 - - + -
103B THR* 1.3 75.5 - - - +
105B GLN* 1.3 61.9 + - - +
115B LEU* 3.6 26.0 - - + -
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Residues in contact with GLN 105 (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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23B LEU* 4.0 4.5 - - - -
28B ARG* 3.2 21.2 - - + +
29B THR* 3.9 18.2 - - + +
62B VAL* 3.4 2.8 - - - -
63B GLU* 2.9 47.9 + - + +
65B LEU* 3.2 39.7 - - + +
103B THR 4.1 0.2 + - - -
104B PHE* 1.3 76.5 - - - +
106B LEU* 1.3 71.0 + - - +
107B ARG* 3.0 8.7 + - - +
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Residues in contact with LEU 106 (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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23B LEU* 3.8 15.7 - - + +
24B SER* 3.6 32.8 - - - +
28B ARG* 2.8 50.0 + - + +
60B HIS* 4.2 2.7 - - + -
61B ARG 3.7 10.1 - - - +
62B VAL* 4.1 10.1 - - + +
105B GLN* 1.3 70.8 + - - +
107B ARG* 1.3 60.3 + - - +
108B ALA 3.3 24.2 - - - +
109B GLY 3.4 19.3 - - - +
111B GLY* 3.9 13.0 - - - +
113B VAL* 3.7 22.7 - - + -
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Residues in contact with ARG 107 (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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28B ARG* 4.5 4.7 + - - -
61B ARG* 2.8 49.1 + - - +
63B GLU* 3.3 46.1 + - + +
105B GLN* 3.0 9.2 + - - +
106B LEU* 1.3 73.5 - - - +
108B ALA* 1.3 58.3 - - - +
53C GLU* 3.8 14.3 + - - -
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Residues in contact with ALA 108 (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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28B ARG* 4.1 3.4 - - - +
59B MET 3.9 9.4 - - - +
60B HIS* 3.2 2.9 - - - -
61B ARG* 3.0 30.6 + - + -
106B LEU* 3.3 11.0 - - - +
107B ARG* 1.3 79.5 - - - +
109B GLY* 1.3 62.0 + - - +
53C GLU* 3.7 38.4 - - + +
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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