Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 3CFV
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 GLN 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 1.3 79.9 - - - +
48A TRP* 1.3 75.0 + - - +
49A LEU 3.5 0.3 + - - -
65A LEU* 3.6 4.0 - - - +
66A VAL* 2.8 42.3 + - + +
129A ALA 4.3 8.5 - - - +
130A ARG* 3.1 34.3 - - - +
131A TYR* 2.8 51.7 + - + +
380A SER* 3.5 9.2 - - - +
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Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 1.3 74.6 - - - +
49A LEU* 1.3 64.5 + - - +
63A HIS* 3.5 26.2 - + + -
64A TRP 3.4 10.5 - - - -
65A LEU* 3.3 36.8 - - + -
83A VAL* 4.1 2.2 - - + -
85A ILE* 4.0 3.8 - - + -
131A TYR* 3.3 21.0 + - - -
380A SER* 2.9 49.0 + - - +
381A TRP 3.2 15.9 - - - +
382A ASN* 3.3 37.8 - - + +
383A PRO* 3.6 20.5 - - + +
388A VAL* 4.2 4.5 - - + -
390A CYS* 3.5 26.8 - - + +
400A ILE* 3.9 28.5 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN 3.5 0.2 + - - -
48A TRP* 1.3 82.1 - - - +
50A PRO* 1.3 66.4 - - + +
51A GLU* 3.2 27.4 + - - +
63A HIS* 6.1 0.2 - - - +
64A TRP* 2.7 42.1 + - + +
66A VAL* 3.1 31.6 - - + +
80A VAL* 3.8 20.2 - - + -
131A TYR* 3.9 22.9 - - + -
136A PRO 4.3 8.3 - - - +
139A ILE* 5.5 0.9 - - + -
153A TYR* 4.4 20.4 - - + +
383A PRO* 4.0 5.8 - - - +
384A ASN* 4.5 0.5 - - - +
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Residues in contact with PRO 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 1.3 89.3 - - + +
51A GLU* 1.3 69.6 + - + +
52A VAL* 3.7 1.0 + - - +
131A TYR* 3.7 28.2 - - + +
133A PRO 5.9 0.4 - - - +
136A PRO* 3.6 30.1 - - + -
383A PRO* 4.3 12.8 - - + -
384A ASN* 2.8 23.4 + - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.2 35.0 - - - +
50A PRO* 1.3 90.6 - - + +
52A VAL* 1.3 61.7 + - - +
62A LEU 4.2 1.2 - - - +
63A HIS* 4.2 6.4 + - - +
64A TRP* 3.4 31.4 + - + -
136A PRO* 3.7 18.6 - - - +
153A TYR* 4.7 9.3 + - - -
384A ASN* 4.1 1.0 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO 3.7 0.4 + - - +
51A GLU* 1.3 76.3 - - - +
53A THR* 1.3 73.0 + - - +
54A LYS* 4.7 16.2 - - - +
61A ALA* 4.8 1.1 - - + -
62A LEU 3.4 14.1 - - - +
63A HIS* 3.6 27.4 - - + +
64A TRP* 4.3 2.5 - - - -
384A ASN* 3.4 35.9 - - + +
385A GLU* 6.1 0.2 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 1.3 80.1 - - - +
54A LYS* 1.3 66.9 + - - +
55A PRO* 3.3 8.4 - - + +
61A ALA* 3.6 1.7 - - - +
62A LEU* 2.8 65.0 + - + -
64A TRP* 4.1 9.4 - - + -
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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