Contacts of the strand formed by residues 116 - 120 (chain I) in PDB entry 4B3E
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 THR 116 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I HIS 3.8 0.2 - - - +
47I VAL* 3.5 4.7 - - - -
48I HIS* 2.7 36.7 + - - +
50I PHE 2.5 27.0 + - - -
51I GLY* 3.2 11.6 - - - -
52I ASP 3.9 3.5 + - - -
60I ALA* 3.8 20.8 - - + +
115I ARG* 1.3 76.8 - - - +
117I LEU* 1.3 71.6 + - - +
118I VAL* 3.8 4.0 - - + -
146I CYS* 3.5 20.6 - - + -
147I GLY 3.3 15.3 + - - +
148I VAL* 4.6 2.4 - - - +
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Residues in contact with LEU 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I CYS* 3.8 22.6 - - + -
8I LEU* 3.3 8.9 - - + +
18I ILE* 3.8 35.4 - - + -
20I PHE* 4.1 17.0 - - + -
45I PHE* 3.8 37.0 - - + -
46I HIS 3.5 20.4 - - - +
47I VAL* 4.4 13.9 - - + +
84I LEU* 4.5 4.7 - - + -
115I ARG 4.2 1.0 + - - -
116I THR* 1.3 72.7 - - - +
118I VAL* 1.3 61.3 + - - +
146I CYS* 3.1 25.5 - - - +
147I GLY 3.0 9.1 + - - -
148I VAL 5.4 0.2 - - - -
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Residues in contact with VAL 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLY 3.7 0.7 - - - +
45I PHE* 3.4 9.5 - - - -
46I HIS 2.9 28.9 + - - -
48I HIS* 3.5 33.0 - - + +
60I ALA* 4.8 4.7 - - + -
116I THR* 3.8 16.8 - - + -
117I LEU* 1.3 81.5 - - - +
119I VAL* 1.3 64.9 + - - +
120I HIS* 3.5 25.3 - - + +
143I ARG* 3.8 31.4 - - + -
145I ALA 3.5 5.8 - - - +
146I CYS* 3.9 7.0 - - + -
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Residues in contact with VAL 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 4.3 13.8 - - + +
14I VAL* 3.9 15.7 - - + -
35I ILE* 4.4 9.9 - - + -
38I LEU* 4.1 13.5 - - + -
43I HIS* 3.9 19.1 - - + -
44I GLY 3.4 9.2 - - - +
45I PHE* 4.2 10.1 - - + -
87I VAL* 4.2 14.8 - - + -
118I VAL* 1.3 75.9 - - - +
120I HIS* 1.3 62.3 + - - +
144I LEU* 2.9 24.6 + - + -
145I ALA* 3.1 30.3 + - + +
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Residues in contact with HIS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I HIS* 2.7 34.7 + - - +
44I GLY 2.8 22.6 + - - +
46I HIS* 3.1 36.7 + + - -
48I HIS* 3.5 11.9 + + - -
63I HIS* 5.1 1.8 - - - -
118I VAL* 3.5 19.5 - - + +
119I VAL* 1.3 74.0 - - - +
121I GLU* 1.3 54.3 + - - +
122I LYS 3.4 0.2 - - - -
137I THR* 5.9 4.3 - - - -
140I ALA* 3.4 25.3 - - + +
141I GLY 2.9 25.8 + - - -
142I SER 3.1 8.1 + - - -
143I ARG* 3.9 22.0 - - + -
144I LEU* 3.8 6.9 - - - +
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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