Contacts of the strand formed by residues 138 - 143 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C SER* 3.9 2.0 - - - -
76C ILE* 3.1 27.4 - - + +
78C LEU* 4.4 9.4 - - + -
133C LEU* 4.0 44.2 - - + -
136C LYS 3.8 12.8 - - - +
137C ASP* 1.3 75.9 - - - +
139C SER* 1.3 71.5 + - - +
140C ILE* 4.2 16.4 - - + -
159C PHE* 4.7 3.4 - + - -
162C LEU* 4.6 6.1 - - + -
163C LEU* 3.6 47.1 - - + +
166C LYS* 4.1 19.5 - - + -
167C TYR* 3.2 6.1 + + - -
175C ARG* 3.1 25.4 + - - +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ILE* 4.4 6.4 - - - +
73C ASP* 3.8 4.3 + - - -
74C SER* 2.7 23.1 + - - -
76C ILE 3.0 5.3 + - - -
77C LEU* 3.7 13.2 - - - -
78C LEU* 2.9 29.5 + - - +
138C PHE* 1.3 77.0 + - - +
140C ILE* 1.3 66.1 + - - +
163C LEU* 5.0 0.4 - - - -
175C ARG* 3.4 28.4 + - - +
177C TYR* 4.1 15.0 + - - -
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Residues in contact with ILE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 4.3 2.2 - - - -
78C LEU* 3.3 10.8 - - + +
80C VAL* 3.7 25.6 - - + -
138C PHE* 4.2 12.8 - - + -
139C SER* 1.3 77.9 - - - +
141C ASN* 1.3 61.9 + - - +
142C VAL* 3.9 9.4 + - + +
156C PHE* 4.1 19.5 - - + -
159C PHE* 3.7 37.9 - - + +
160C ARG* 4.1 7.6 - - - +
163C LEU* 3.9 19.3 - - + -
175C ARG 2.8 11.6 + - - +
176C ILE* 3.3 7.8 - - + -
177C TYR* 2.8 29.1 + - - +
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Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 4.0 19.4 - - + +
78C LEU 2.9 9.6 + - - +
79C VAL* 3.5 6.9 - - + -
80C VAL 2.9 22.2 + - - -
140C ILE* 1.3 73.5 - - - +
142C VAL* 1.3 61.0 + - - +
143C ILE* 3.5 24.0 + - - +
177C TYR* 2.8 31.1 + - + -
179C THR* 3.3 21.0 + - - -
214C PRO 5.0 0.3 - - - +
218C LEU* 3.6 23.8 - - + +
219C PRO* 3.7 16.3 - - - +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C VAL* 3.7 15.7 - - + +
140C ILE* 3.8 1.6 - - + -
141C ASN* 1.3 72.2 - - - +
143C ILE* 1.3 64.1 + - - +
144C SER* 4.3 2.7 - - - -
152C PRO* 5.2 3.4 - - + +
156C PHE* 3.7 56.3 - - + -
176C ILE* 4.2 7.4 - - + -
177C TYR 2.9 13.5 + - - +
178C ALA* 3.4 15.4 - - + -
179C THR 2.9 25.3 + - - +
187C LEU* 3.9 23.1 - - + +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 3.7 17.3 - - + -
80C VAL 2.9 18.3 + - - +
81C GLY* 3.9 4.7 - - - -
82C ILE 4.9 0.2 + - - -
85C SER* 3.5 48.9 - - - +
89C ALA* 6.0 0.2 - - + -
141C ASN* 3.5 31.6 - - - +
142C VAL* 1.3 79.4 - - - +
144C SER* 1.3 65.8 + - - +
152C PRO* 4.9 3.1 - - - +
179C THR* 3.4 13.9 - - - +
201C ILE* 4.4 1.3 - - + -
215C VAL* 3.6 45.3 - - + +
219C PRO* 4.4 1.6 - - + -
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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