Contacts of the strand formed by residues 119 - 123 (chain B) in PDB entry 3CTP
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 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B THR 4.0 1.6 + - - -
63B ILE* 3.4 9.6 - - - +
64B GLY 3.0 23.2 + - - -
117B VAL* 3.3 4.4 - - - +
118B ALA* 1.3 81.4 - - - +
120B ILE* 1.3 66.1 + - - +
136B ILE* 3.7 3.4 - - - -
137B PRO 3.2 13.7 - - - -
297B LEU* 4.3 13.5 - - - -
301B ILE* 4.4 2.0 - - - +
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Residues in contact with ILE 120 (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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64B GLY 3.3 8.3 - - - +
66B MET* 4.1 20.6 - - + -
109B LEU* 3.7 26.7 - - + +
112B LEU* 3.9 26.2 - - + -
113B GLN* 5.0 0.7 - - + -
117B VAL* 3.9 11.2 - - + -
119B GLY* 1.3 80.0 - - - +
121B ILE* 1.3 74.4 + - - +
122B ALA* 4.1 6.3 - - + +
131B TYR* 5.0 3.4 - - + -
134B ILE* 4.5 7.0 - - + -
136B ILE* 4.4 19.1 - - + -
137B PRO 2.8 9.5 + - - +
138B VAL* 3.2 13.6 - - + +
139B VAL 3.1 23.9 + - - +
297B LEU* 4.0 4.5 - - - +
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Residues in contact with ILE 121 (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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63B ILE* 3.9 19.3 - - + -
64B GLY 2.8 9.6 + - - +
65B LEU* 3.5 24.5 - - + -
66B MET* 2.9 30.8 + - - +
82B ILE* 3.8 26.5 - - + -
120B ILE* 1.3 76.0 - - - +
122B ALA* 1.3 71.1 + - - +
123B SER* 5.2 0.2 - - - -
139B VAL* 3.5 9.4 - - + +
141B PHE* 5.1 5.2 - - + +
293B ILE* 3.7 42.2 - - + -
294B ILE* 4.1 8.3 - - + -
297B LEU* 3.8 12.8 - - + -
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Residues in contact with ALA 122 (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 MET* 4.5 7.0 - - - -
105B GLU* 4.6 0.9 - - - +
120B ILE* 3.8 4.6 - - + +
121B ILE* 1.3 80.4 - - - +
123B SER* 1.3 61.5 + - - +
125B SER* 4.4 4.7 - - - -
131B TYR* 3.6 19.5 - - + +
138B VAL* 4.3 5.2 - - + -
139B VAL 2.9 12.0 + - - +
140B ALA* 3.4 2.3 - - - -
141B PHE 2.8 22.7 + - - -
145B ILE* 3.5 31.9 - - + -
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Residues in contact with SER 123 (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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65B LEU* 5.0 4.7 - - - -
66B MET* 3.0 31.3 + - - +
68B PRO* 3.5 25.0 - - - +
75B PHE* 3.8 5.9 - - - -
98B THR* 4.7 4.9 + - - -
105B GLU* 5.5 0.9 + - - -
121B ILE* 4.0 0.9 + - - -
122B ALA* 1.3 78.1 - - - +
124B ARG* 1.3 70.7 + - - +
125B SER* 3.1 3.3 + - - +
141B PHE* 3.5 28.1 - - - +
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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