Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 4HVY
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 CYS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 1.3 71.6 - - - +
44A TYR* 1.3 64.2 + - - +
45A MET* 3.7 29.6 + - - -
77A ARG* 3.9 25.6 - - - +
114A SER 2.8 16.5 + - - +
115A TRP* 3.5 9.7 - - + -
116A VAL 2.9 27.0 + - - +
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Residues in contact with TYR 44 (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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42A VAL* 3.8 27.1 + - + -
43A CYS* 1.3 71.8 - - - +
45A MET* 1.3 60.3 + - - +
77A ARG* 3.7 8.2 - - - +
78A MET* 3.0 60.6 + - + +
84A ILE* 4.7 9.2 - - + -
116A VAL* 3.4 16.4 - - + -
118A PHE* 3.4 40.7 - + + -
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Residues in contact with MET 45 (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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43A CYS* 3.7 15.5 - - - -
44A TYR* 1.3 74.3 - - - +
46A VAL* 1.3 63.3 + - - +
75A ALA* 5.6 1.1 - - + -
76A GLY* 3.5 12.1 - - - +
77A ARG* 3.5 39.0 - - + +
78A MET 4.6 0.4 - - - +
84A ILE* 4.6 2.5 - - - -
115A TRP* 3.4 33.9 - - + +
116A VAL 2.8 10.1 + - - +
117A ARG* 3.4 14.7 - - + +
118A PHE* 2.8 31.3 + - - -
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Residues in contact with VAL 46 (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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45A MET* 1.3 76.6 - - - +
47A LEU* 1.3 65.7 + - - +
75A ALA* 3.2 3.6 - - - +
76A GLY 2.9 40.5 + - - +
78A MET 5.2 0.2 - - - +
84A ILE* 3.8 15.0 - - + -
87A ALA* 3.9 12.6 - - + +
88A LEU* 3.8 39.7 - - + +
91A VAL* 4.0 11.2 - - + -
117A ARG* 5.0 0.9 - - - -
118A PHE 3.3 5.2 - - - +
120A PHE* 3.6 34.8 - - + -
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Residues in contact with LEU 47 (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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46A VAL* 1.3 76.6 - - - +
48A ALA* 1.3 62.5 + - - +
49A VAL* 3.8 12.1 - - + -
72A TYR* 3.9 31.4 - - + +
73A LEU* 3.4 31.2 - - + -
74A PRO 3.3 12.3 - - - +
75A ALA* 4.2 4.3 - - + -
88A LEU* 4.1 4.6 - - - +
117A ARG* 4.3 21.1 - - + +
118A PHE 2.9 9.5 + - - +
119A VAL* 3.5 6.6 - - + -
120A PHE* 2.9 28.9 + - - +
159A ILE* 4.2 1.6 - - + -
162A LEU* 3.8 26.7 - - + -
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Residues in contact with ALA 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 LEU* 1.3 75.4 - - - +
49A VAL* 1.3 61.7 + - - +
50A PHE* 3.7 14.6 - - + -
73A LEU* 3.5 7.6 - - - +
74A PRO* 2.9 26.4 + - + +
88A LEU* 3.5 22.2 - - + +
92A VAL* 3.7 22.0 - - + -
120A PHE 3.6 3.6 - - - +
122A ALA* 4.6 3.4 - - + -
203A MG 2.9 13.7 - - - -
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Residues in contact with VAL 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 LEU* 3.8 8.7 - - + -
48A ALA* 1.3 74.7 - - - +
50A PHE* 1.3 71.7 + - - +
51A LEU* 4.9 1.8 - - + -
57A VAL* 4.9 0.7 - - + -
73A LEU* 3.8 21.3 - - + -
106A LEU* 4.3 8.5 - - + -
119A VAL* 3.9 16.2 - - + -
120A PHE 2.8 12.7 + - - +
121A LEU* 3.3 7.8 - - - +
122A ALA 2.9 23.4 + - - -
162A LEU* 4.2 12.8 - - + +
163A VAL* 4.3 19.3 - - + -
166A ALA* 3.5 26.0 - - + -
203A MG 3.4 3.1 - - - -
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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