Contacts of the strand formed by residues 92 - 98 (chain C) in PDB entry 2IVF
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 GLY 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C TRP* 4.1 0.9 - - - -
90C VAL 3.8 0.8 + - - -
91C ASP* 1.3 75.6 - - - +
93C VAL* 1.3 60.4 + - - -
119C TYR* 4.7 3.4 - - - -
120C TRP* 3.0 19.9 - - - -
121C LYS* 4.3 2.0 - - - -
189C VAL* 3.1 10.2 - - - +
190C TRP* 2.9 44.1 + - - +
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Residues in contact with VAL 93 (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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58C LEU* 4.2 8.5 - - + -
73C LEU* 3.8 28.9 - - + -
75C TRP* 3.6 22.4 - - + -
92C GLY* 1.3 74.1 - - - +
94C GLY* 1.3 61.0 + - - +
118C TRP 3.8 0.5 - - - +
119C TYR* 3.7 1.9 - - - -
120C TRP* 2.9 55.2 + - + +
162C VAL* 4.2 11.4 - - + -
164C LEU* 4.5 6.4 - - + +
188C ALA 3.3 14.6 - - - +
189C VAL* 4.0 13.2 - - + -
190C TRP* 3.7 6.9 - - - -
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Residues in contact with GLY 94 (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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73C LEU* 5.3 0.4 - - - -
93C VAL* 1.3 77.3 - - - +
95C ALA* 1.3 59.9 + - - -
117C ALA* 5.6 0.2 - - - -
118C TRP 3.2 9.6 - - - -
119C TYR* 4.5 2.9 - - - -
164C LEU* 5.3 1.1 - - - -
187C PHE* 3.2 11.0 - - - +
188C ALA 2.8 31.0 + - - +
190C TRP* 3.6 10.8 - - - -
1217C HEM 3.8 14.4 - - - -
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Residues in contact with ALA 95 (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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71C LEU* 3.5 33.0 - - + -
73C LEU* 5.0 1.3 - - + -
94C GLY* 1.3 73.0 - - - -
96C MET* 1.3 61.1 + - - +
97C PHE* 3.8 13.8 - - + -
117C ALA* 3.2 2.6 - - - -
118C TRP* 2.8 37.1 + - + +
164C LEU* 4.7 9.1 - - + +
185C ILE* 4.7 0.4 - - + -
186C ALA 3.4 4.7 - - - -
187C PHE* 3.7 15.0 - - + -
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Residues in contact with MET 96 (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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95C ALA* 1.3 73.0 - - - +
97C PHE* 1.3 68.7 + - - +
105C ALA* 3.5 29.6 - - + +
108C MET* 4.4 13.0 - - - -
115C VAL* 3.5 33.0 - - + -
116C ASN 3.5 9.2 - - - +
117C ALA* 4.0 7.2 - - + +
185C ILE* 3.3 8.7 - - - +
186C ALA 2.6 37.3 + - - +
207C PHE* 3.3 30.2 - - + -
1217C HEM 3.8 34.1 - - + +
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Residues in contact with PHE 97 (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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71C LEU* 4.2 9.0 - - + -
95C ALA* 3.8 15.0 - - + -
96C MET* 1.3 75.1 - - - +
98C PRO* 1.3 70.1 - - + +
115C VAL* 3.3 2.9 - - - +
116C ASN* 2.7 42.3 + - - +
118C TRP* 3.7 45.1 - + - -
175C ALA* 3.4 27.1 - - + -
177C LEU* 3.9 25.8 - - + -
183C SER* 4.2 3.8 - - - +
184C LYS 3.4 16.8 - - - +
185C ILE* 3.6 29.4 - - + -
207C PHE* 3.8 4.9 - - - -
210C PHE* 4.1 9.2 - + - -
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Residues in contact with PRO 98 (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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97C PHE* 1.3 89.1 - - + +
99C VAL* 1.3 63.7 + - - +
100C ALA 3.8 17.0 - - - +
103C ALA* 4.0 5.6 - - + +
114C PRO 4.0 4.3 - - - +
115C VAL* 4.2 1.6 - - + -
175C ALA* 4.4 4.9 - - - +
176C LYS 5.1 1.6 + - - -
183C SER* 3.8 11.0 + - - +
184C LYS* 3.3 37.7 - - + +
207C PHE* 3.6 27.5 - - + -
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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