Contacts of the strand formed by residues 138 - 143 (chain E) in PDB entry 3IFS
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 PHE 138 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E SER* 3.8 1.8 - - - -
76E ILE* 3.2 26.7 - - + +
78E LEU* 4.7 8.1 - - + -
133E LEU* 3.9 42.6 - - + -
136E LYS 3.9 11.9 - - - +
137E ASP* 1.3 75.7 - - - +
139E SER* 1.3 73.0 + - - +
140E ILE* 4.1 15.0 - - + -
159E PHE* 4.5 3.8 - + - -
162E LEU* 4.5 8.5 - - + -
163E LEU* 3.6 45.5 - - + +
166E LYS* 4.0 22.2 - - + -
167E TYR* 3.1 6.5 + + - -
175E ARG* 3.1 25.3 + - - -
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Residues in contact with SER 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 5.5 0.2 + - - -
70E ILE* 4.4 6.4 - - - +
73E ASP* 3.8 4.5 + - - -
74E SER* 2.6 24.1 + - - -
76E ILE 3.1 5.3 + - - +
77E LEU* 3.7 13.4 - - - -
78E LEU* 2.9 28.9 + - - +
138E PHE* 1.3 75.5 + - - +
140E ILE* 1.3 64.5 + - - +
163E LEU* 5.0 0.2 - - - -
175E ARG* 3.3 26.7 + - - +
177E TYR* 4.1 16.0 + - - -
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Residues in contact with ILE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 4.2 2.2 - - - -
78E LEU* 3.3 9.4 - - + +
80E VAL* 3.8 25.1 - - + -
138E PHE* 4.1 13.0 - - + -
139E SER* 1.3 79.6 - - - +
141E ASN* 1.3 61.8 + - - +
142E VAL* 4.0 8.1 - - + +
156E PHE* 4.1 17.7 - - + -
159E PHE* 3.6 39.0 - - + +
160E ARG* 3.9 11.7 - - + +
163E LEU* 4.0 17.5 - - + -
175E ARG 2.9 10.3 + - - +
176E ILE* 3.4 7.6 - - + +
177E TYR* 2.9 28.7 + - - +
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Residues in contact with ASN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 3.9 21.9 - - + +
78E LEU 2.9 9.6 + - - +
79E VAL* 3.4 6.1 - - + -
80E VAL 2.8 24.3 + - - +
140E ILE* 1.3 71.9 - - - +
142E VAL* 1.3 62.0 + - - +
143E ILE* 3.5 23.8 + - - +
177E TYR* 2.8 25.0 + - + +
179E THR* 3.3 22.0 + - - -
214E PRO 5.1 0.3 - - - +
218E LEU* 3.6 24.1 - - + +
219E PRO* 3.7 13.9 - - - +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E VAL* 3.5 20.0 - - + +
140E ILE* 3.8 1.9 - - + -
141E ASN* 1.3 72.4 - - - +
143E ILE* 1.3 63.8 + - - +
144E SER* 4.2 3.4 - - - -
152E PRO* 5.0 3.6 - - + +
156E PHE* 3.6 54.5 - - + -
176E ILE* 4.5 4.0 - - + -
177E TYR 3.0 11.4 + - - +
178E ALA* 3.5 10.7 - - + -
179E THR 2.9 24.6 + - - +
187E LEU* 4.0 24.4 - - + +
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Residues in contact with ILE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E VAL* 3.9 15.5 - - + -
80E VAL 2.8 19.4 + - - +
81E GLY* 3.9 4.9 - - - -
82E ILE 5.0 0.3 + - - -
85E SER* 3.5 47.3 - - - +
141E ASN* 3.5 30.7 - - - +
142E VAL* 1.3 78.5 - - - +
144E SER* 1.3 65.9 + - - +
152E PRO* 4.7 2.9 - - - +
179E THR* 3.4 15.5 - - - +
201E ILE* 4.1 2.2 - - + -
215E VAL* 3.6 46.7 - - + +
219E PRO* 4.8 1.3 - - + -
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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