Contacts of the strand formed by residues 53 - 58 (chain B) in PDB entry 3JW8
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 ALA 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PRO* 3.4 5.5 - - - +
52B LYS* 1.4 81.3 - - - +
54B LEU* 1.3 64.1 + - - +
79B ASP 4.0 1.4 + - - -
80B LEU* 3.4 12.3 - - + +
81B LEU* 2.9 24.9 + - - +
124B LEU* 4.3 5.6 - - - -
125B PRO* 3.4 21.5 - - + +
127B PHE* 3.9 25.4 - - + -
304B THR* 4.0 12.3 - - + -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 1.3 73.9 - - - +
55B ILE* 1.3 63.2 + - - +
80B LEU* 4.5 0.7 - - - -
81B LEU* 3.4 27.8 - - + +
83B PHE* 3.9 12.3 - - + -
117B MSE 4.2 36.3 - - + +
118B GLN* 4.2 19.3 - - + -
121B TYR* 4.2 23.8 - - + +
124B LEU* 4.0 25.8 - - + +
125B PRO 3.0 12.3 + - - +
126B VAL* 3.4 10.0 - - + -
127B PHE* 2.8 27.9 + - - -
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 1.3 75.1 - - - +
56B PHE* 1.3 69.7 + - - +
57B VAL* 3.9 1.0 + - + -
75B LEU* 4.2 28.7 - - + -
80B LEU* 3.8 19.1 - - + -
81B LEU 3.0 5.6 + - - +
82B VAL* 3.4 31.3 - - + +
83B PHE* 2.9 29.1 + - - +
127B PHE* 3.3 31.6 - - + +
128B LEU 4.2 4.7 - - - +
129B LEU* 4.2 18.8 - - + +
153B VAL* 5.1 3.4 - - + -
300B VAL* 4.4 13.7 - - + -
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Residues in contact with PHE 56 (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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55B ILE* 1.3 72.3 - - - +
57B VAL* 1.3 79.5 + - - +
58B SER* 3.7 14.6 - - - -
83B PHE* 3.2 43.7 - + + -
84B ALA* 3.8 7.9 - - - -
85B HIS* 3.6 47.6 - + - -
87B HIS* 4.7 1.8 - + - -
110B VAL* 3.7 36.1 - - + -
113B HIS* 3.8 9.6 - + + -
114B VAL* 4.3 4.5 - - + -
126B VAL* 5.4 0.2 - - + -
127B PHE 3.0 7.6 + - - +
128B LEU* 3.5 19.8 - - + -
129B LEU* 2.9 28.8 + - - +
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Residues in contact with VAL 57 (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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45B TRP* 5.3 2.2 - - + -
55B ILE* 4.6 2.0 - - + +
56B PHE* 1.3 88.2 - - - +
58B SER* 1.4 61.0 + - - +
59B HIS* 4.1 2.0 + - + +
65B SER* 5.6 1.8 - - - +
68B TYR* 3.6 47.6 - - + -
71B LEU* 6.4 0.9 - - + -
72B ALA* 5.4 1.8 - - + +
75B LEU* 4.9 9.4 - - + -
82B VAL* 3.6 28.0 - - + -
83B PHE 2.9 12.9 + - - +
84B ALA* 3.4 23.7 - - + +
85B HIS 4.6 2.3 + - - +
129B LEU* 3.5 22.9 - - + -
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Residues in contact with SER 58 (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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56B PHE* 3.7 17.0 - - - -
57B VAL* 1.4 72.2 - - - +
59B HIS* 1.3 62.0 + - - +
68B TYR* 4.6 1.6 + - - -
85B HIS 5.9 0.2 - - - -
87B HIS* 3.3 18.1 + - - -
110B VAL* 5.3 0.2 - - - -
128B LEU* 6.4 0.4 - - - -
129B LEU 2.8 16.2 + - - -
130B GLY* 3.5 1.3 - - - -
131B HIS 3.3 21.7 + - - -
134B GLY* 3.0 30.1 + - - -
137B ILE* 3.7 10.9 - - - +
138B ALA* 4.9 5.4 - - - -
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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
------------------------------------------------------------
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