Contacts of the strand formed by residues 58 - 62 (chain B) in PDB entry 3C3P
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 LEU 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLN* 1.3 80.1 - - + +
59B VAL* 1.3 71.8 + - - +
60B VAL* 4.0 9.2 - - + -
82B ARG* 3.5 12.8 - - + +
84B VAL* 3.8 29.4 - - + -
123B GLN* 3.8 17.9 - - + +
124B ARG 3.2 27.8 - - - +
125B ASP 3.9 11.0 - - - +
126B ILE* 3.9 18.1 - - + +
127B ASP* 2.9 32.9 + - - +
128B ILE 3.2 6.6 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 3.5 32.8 - - + -
58B LEU* 1.3 75.2 - - - +
60B VAL* 1.3 60.3 + - - +
61B VAL* 4.3 7.6 - - + -
73B PHE* 3.8 37.2 - - + -
77B ILE* 4.7 7.0 - - + -
82B ARG 2.9 14.7 + - - +
83B VAL* 3.3 14.4 - - + +
84B VAL 2.7 32.1 + - - +
128B ILE* 3.4 27.6 - - + +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.0 11.0 - - + -
59B VAL* 1.3 77.8 - - - +
61B VAL* 1.3 67.9 + - - +
62B PRO* 3.6 4.0 - - + +
84B VAL* 3.5 10.3 - - + +
86B ILE* 4.5 5.6 - - + -
120B ALA* 3.8 31.9 - - + -
123B GLN* 4.0 16.8 - - + -
126B ILE* 3.6 38.4 - - + -
128B ILE 2.9 9.5 + - - +
129B LEU* 3.7 10.3 - - + -
130B PHE* 3.0 27.4 + - - +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 4.3 2.7 - - + -
60B VAL* 1.3 79.0 - - - +
62B PRO* 1.4 58.5 - - - +
63B GLY 3.2 11.2 + - - +
64B ASP* 3.7 33.0 - - + +
69B ALA* 4.1 2.7 - - + -
70B SER* 4.0 9.2 - - - +
73B PHE* 4.0 25.4 - - + -
83B VAL* 3.9 24.5 - - + -
84B VAL 2.8 12.9 + - - +
85B MSE 3.5 1.9 - - + +
86B ILE* 3.1 24.0 + - - +
130B PHE* 3.8 19.5 - - + -
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Residues in contact with PRO 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 3.6 8.1 - - + +
61B VAL* 1.4 76.9 - - + +
63B GLY* 1.3 61.5 + - - +
86B ILE* 3.9 5.4 - - + +
116B PRO* 3.7 31.2 - - + +
117B LEU* 3.9 24.0 - - + -
120B ALA* 4.1 7.9 - - + -
129B LEU* 4.1 12.3 - - + -
130B PHE* 2.9 29.7 - - + +
131B MSE 5.1 6.5 - - + -
132B ASP* 5.5 1.9 + - - +
136B PHE* 3.2 20.9 - - + -
141B VAL* 5.8 0.9 - - + -
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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