Contacts of the strand formed by residues 138 - 144 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B SER* 3.8 1.6 - - - -
76B ILE* 3.1 28.3 - - + +
78B LEU* 4.5 7.9 - - + -
133B LEU* 4.1 42.8 - - + -
136B LYS 3.9 11.7 - - - -
137B ASP* 1.3 75.2 - - - +
139B SER* 1.3 72.3 + - - +
140B ILE* 4.2 16.4 - - + -
159B PHE* 4.7 2.7 - + - -
162B LEU* 4.6 9.2 - - + -
163B LEU* 3.6 47.0 - - + +
166B LYS* 4.2 18.2 - - + -
167B TYR* 3.2 5.5 + - - -
175B ARG* 3.0 26.1 + - - +
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Residues in contact with SER 139 (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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70B ILE* 4.3 9.3 - - - +
73B ASP* 3.8 4.9 + - - -
74B SER* 2.6 25.1 + - - -
76B ILE 3.1 4.8 + - - +
77B LEU* 3.7 14.8 - - - +
78B LEU* 2.9 29.5 + - - +
138B PHE* 1.3 75.2 + - - +
140B ILE* 1.3 64.7 + - - +
163B LEU* 5.0 0.4 - - - -
175B ARG* 3.3 26.2 + - - +
177B TYR* 4.2 11.5 + - - -
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Residues in contact with ILE 140 (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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77B LEU* 4.2 2.7 - - - -
78B LEU* 3.3 11.0 - - + +
80B VAL* 3.7 27.1 - - + -
138B PHE* 4.2 13.5 - - + -
139B SER* 1.3 78.3 - - - +
141B ASN* 1.3 63.9 + - - +
142B VAL 3.9 8.1 - - - +
156B PHE* 4.1 16.6 - - + -
159B PHE* 3.7 40.8 - - + +
160B ARG* 4.0 6.3 - - - +
163B LEU* 4.0 19.7 - - + -
175B ARG 2.8 12.0 + - - +
176B ILE* 3.4 10.1 - - + -
177B TYR* 2.9 29.0 + - - -
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Residues in contact with ASN 141 (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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77B LEU* 4.0 19.6 - - + +
78B LEU 2.9 9.0 + - - +
79B VAL* 3.5 6.6 - - + -
80B VAL 2.9 24.6 + - - +
140B ILE* 1.3 74.5 - - - +
142B VAL* 1.3 62.8 + - - +
143B ILE* 3.6 16.7 + - - +
177B TYR* 2.9 20.1 + - + -
179B THR* 3.4 21.6 + - - -
214B PRO 5.1 0.5 - - - +
218B LEU* 3.6 22.6 - - + +
219B PRO* 3.6 28.1 - - - +
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Residues in contact with VAL 142 (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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80B VAL* 3.6 16.4 - - + +
140B ILE* 3.9 1.8 - - + -
141B ASN* 1.3 72.4 + - - +
143B ILE* 1.3 63.0 + - - +
144B SER* 4.4 1.1 - - - -
152B PRO* 4.9 4.9 - - + +
156B PHE* 3.7 53.4 - - + -
176B ILE* 4.6 3.1 - - + -
177B TYR 2.9 8.3 + - - +
178B ALA* 3.7 24.2 - - + +
179B THR 2.9 25.6 + - - +
187B LEU* 3.9 25.6 - - + +
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Residues in contact with ILE 143 (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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79B VAL* 3.7 20.0 - - + -
80B VAL 2.8 19.7 + - - +
81B GLY* 3.7 6.1 - - - -
82B ILE 4.8 0.2 + - - -
85B SER* 3.4 45.4 - - - +
89B ALA* 6.0 0.7 - - + -
141B ASN* 3.6 31.6 - - - +
142B VAL* 1.3 80.0 - - - +
144B SER* 1.3 66.3 + - - +
152B PRO* 4.7 3.3 - - - +
179B THR* 3.3 14.1 - - - +
187B LEU* 4.7 0.4 - - - -
201B ILE* 4.4 0.7 - - + -
215B VAL* 3.6 44.4 - - + +
219B PRO* 4.4 2.2 - - + -
452B SO4 4.6 1.2 + - - -
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Residues in contact with SER 144 (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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85B SER* 4.0 0.4 - - - -
142B VAL* 5.7 1.1 - - - -
143B ILE* 1.3 78.3 - - - +
145B LYS* 1.3 58.6 + - - +
147B GLY* 2.8 35.7 + - - -
148B THR 3.8 0.2 + - - -
149B THR* 3.8 5.2 + - - -
152B PRO* 5.1 9.0 - - - -
179B THR 3.0 6.9 + - - -
180B THR* 2.8 30.5 + - - -
187B LEU* 4.1 11.7 - - - +
201B ILE* 3.8 3.4 - - - -
452B SO4 3.0 23.3 + - - -
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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