Contacts of the strand formed by residues 76 - 80 (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 ILE 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C SER* 3.3 8.1 - - - -
75C ASP* 1.3 93.1 - - + +
77C LEU* 1.3 74.6 - - - +
78C LEU* 4.3 2.0 - - - +
112C PRO* 4.4 1.6 - - - -
113C GLN* 3.3 32.1 - - + +
115C LEU* 4.0 21.3 - - + -
132C VAL* 3.8 28.5 - - + +
133C LEU* 3.9 23.8 - - + -
136C LYS* 4.1 14.1 - - + -
137C ASP 3.1 2.9 + - - +
138C PHE* 3.1 12.2 - - + +
139C SER 3.0 23.6 + - - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.4 17.0 - - + -
76C ILE* 1.3 75.2 - - - +
78C LEU* 1.3 63.0 + - - +
79C VAL* 3.9 17.6 + - + -
112C PRO* 4.3 0.6 - - + +
113C GLN 2.9 13.5 + - - +
114C VAL* 3.4 8.1 - - + +
115C LEU 2.9 26.7 + - - +
139C SER* 3.7 21.8 - - - +
140C ILE 4.3 0.7 - - - -
141C ASN* 4.0 27.1 - - + +
177C TYR* 5.4 0.2 - - + -
218C LEU* 5.7 0.7 - - + -
219C PRO* 4.0 19.1 - - + -
222C VAL* 3.8 42.0 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 4.0 4.4 - - + -
77C LEU* 1.3 73.4 - - - +
79C VAL* 1.3 59.6 + - - +
80C VAL* 3.8 3.9 + - + -
115C LEU* 3.7 21.1 - - + +
117C VAL* 3.7 19.7 - - + -
129C LEU* 3.6 27.8 - - + -
133C LEU* 4.4 7.0 - - + -
138C PHE* 4.4 18.6 - - + -
139C SER 2.9 15.8 + - - +
140C ILE* 3.3 11.0 - - + +
141C ASN 2.9 24.6 + - - +
159C PHE* 3.7 42.8 - - + -
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.1 10.5 - - + -
78C LEU* 1.3 73.7 - - - +
80C VAL* 1.3 64.3 + - - +
81C GLY 3.8 1.4 + - - +
85C SER 4.3 9.6 - - - +
86C TYR* 5.6 0.9 - - - -
89C ALA* 5.7 1.1 - - + -
114C VAL* 4.0 26.2 - - + -
115C LEU 2.8 9.5 + - - +
116C PHE* 3.4 27.2 - - + +
117C VAL 2.9 26.2 + - - +
141C ASN* 3.5 6.5 - - + +
143C ILE* 3.7 28.3 - - + -
219C PRO* 4.1 22.0 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 4.3 7.2 - - + +
79C VAL* 1.3 76.1 - - - +
81C GLY* 1.3 60.6 + - - +
117C VAL* 3.2 23.1 - - + +
140C ILE* 3.7 27.8 - - + -
141C ASN 2.9 6.9 + - - +
142C VAL* 4.0 11.6 - - + +
143C ILE* 2.9 31.7 + - - +
152C PRO* 3.5 33.3 - - + +
155C ALA* 4.3 5.8 - - + +
156C PHE* 3.9 22.7 - - + +
159C PHE* 5.4 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