Contacts of the strand formed by residues 113 - 117 (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 GLN 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C ASP* 3.0 13.4 + - - +
76C ILE* 3.3 33.2 - - + +
77C LEU 2.9 25.3 + - - -
101C TYR* 4.1 0.7 - - - -
102C ASN* 2.8 44.4 + - - +
104C LEU 5.1 0.8 + - - -
109C ARG* 3.4 32.7 - - - +
112C PRO* 1.3 76.7 - - - +
114C VAL* 1.3 59.2 - - - +
115C LEU* 4.1 5.8 - - + -
132C VAL* 4.6 5.8 - - - +
136C LYS* 5.1 8.8 + - - +
103D THR* 4.0 18.2 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.4 16.4 - - + +
79C VAL* 4.0 20.0 - - + -
93C ILE* 4.0 19.0 - - + +
101C TYR* 4.0 6.3 - - + -
102C ASN* 3.1 25.6 + - - -
112C PRO 3.7 8.9 + - - +
113C GLN* 1.3 78.2 - - - +
115C LEU* 1.3 62.2 + - - +
116C PHE* 3.9 32.3 - - + -
219C PRO* 4.6 4.9 - - + +
222C VAL* 4.7 4.3 - - + -
223C SER* 4.3 23.8 - - - -
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Residues in contact with LEU 115 (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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76C ILE* 4.0 23.6 - - + -
77C LEU 2.9 9.3 + - - +
78C LEU* 3.4 9.3 - - + -
79C VAL* 2.8 27.5 + - - +
102C ASN* 3.5 31.0 - - + +
113C GLN* 4.7 4.7 - - + +
114C VAL* 1.3 75.0 - - - +
116C PHE* 1.3 65.5 + - - +
129C LEU* 3.4 32.1 - - + -
132C VAL* 3.7 25.1 - - + -
133C LEU* 4.8 1.8 - - + -
100D PHE* 4.5 19.1 - - + -
103D THR* 5.5 4.5 - - + +
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Residues in contact with PHE 116 (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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78C LEU* 4.4 1.1 - - - -
79C VAL* 3.4 36.6 - - + +
86C TYR* 3.5 44.2 - + + -
89C ALA* 4.6 5.4 - - + -
90C ARG* 3.8 56.3 - - + +
93C ILE* 4.3 10.3 - - + -
94C GLU* 5.7 0.7 - - + -
114C VAL* 3.9 29.4 - - + -
115C LEU* 1.3 77.6 - - - +
117C VAL* 1.3 62.8 + - - +
119C GLN* 3.7 6.7 - - - +
125C TYR* 2.6 34.1 + - - +
129C LEU* 4.4 2.6 - - - +
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Residues in contact with VAL 117 (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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78C LEU* 3.7 24.0 - - + -
79C VAL 2.9 7.9 + - - +
80C VAL* 3.2 23.2 - - + -
81C GLY 3.1 24.6 + - - +
116C PHE* 1.3 76.0 - - - +
118C GLY* 1.3 66.2 + - - +
119C GLN* 3.1 11.8 + - - -
120C ASN* 5.7 0.2 - - - +
125C TYR* 4.2 8.1 - - + -
126C MSE 4.0 18.4 - - + -
129C LEU* 3.7 15.9 - - + -
155C ALA* 4.2 5.6 - - + -
159C PHE* 3.7 31.2 - - + -
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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