Contacts of the strand formed by residues 42 - 49 (chain C) in PDB entry 2IB8
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 VAL 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS 4.0 1.6 - - - +
41C GLU* 1.3 77.4 - - - +
43C VAL* 1.3 67.1 + - - +
137C SER* 3.7 26.9 - - - +
140C LEU* 3.8 34.5 - - + -
141C MET* 3.6 39.4 - - + +
295C LEU* 4.7 2.7 - - + -
296C MET 3.6 3.4 - - - +
311C ARG* 3.7 5.4 - - - +
312C ILE* 2.9 49.6 + - + +
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 4.1 22.2 - - + +
42C VAL* 1.3 81.3 - - - +
44C ILE* 1.3 62.7 + - - +
45C VAL* 3.8 3.3 + - + -
295C LEU* 3.4 5.9 - - - +
296C MET* 2.9 57.0 + - + +
297C THR 4.1 7.0 - - - +
298C ALA* 4.3 7.2 - - + +
301C ALA* 4.3 5.6 - - + -
308C PRO* 3.7 29.2 - - + -
310C ALA 3.2 11.7 - - - +
311C ARG* 4.3 3.6 - - - +
312C ILE 5.3 0.2 - - - -
427C LEU* 4.2 9.4 - - + -
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Residues in contact with ILE 44 (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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43C VAL* 1.3 70.4 - - - +
45C VAL* 1.3 55.7 + - - +
46C SER 3.4 23.3 - - - +
47C ALA* 4.6 0.9 - - + -
293C LEU* 4.1 9.2 - - + -
294C VAL 3.7 5.4 - - - +
295C LEU* 3.7 19.5 - - + -
308C PRO* 3.7 1.1 - - - -
309C LEU* 2.7 32.4 + - - +
310C ALA* 2.7 25.7 + - + +
312C ILE* 3.7 25.4 - - + -
395C VAL* 4.2 11.9 - - + -
399C THR* 3.6 36.8 - - + +
424C ILE* 4.2 15.3 - - + -
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Residues in contact with VAL 45 (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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43C VAL* 4.2 10.3 - - + +
44C ILE* 1.3 75.6 - - - +
46C SER* 1.3 60.8 + - - +
78C LYS 5.0 1.4 - - - +
79C ALA* 4.0 31.5 - - + +
294C VAL* 2.9 14.3 + - + +
296C MET* 3.6 41.3 - - + -
301C ALA* 4.7 0.7 - - + -
306C VAL* 4.1 20.9 - - + -
307C THR 4.5 8.7 - - - +
308C PRO* 4.3 8.1 - - + -
309C LEU* 3.5 21.7 - - - +
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Residues in contact with SER 46 (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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44C ILE* 3.4 13.1 - - - +
45C VAL* 1.3 79.8 - - - +
47C ALA* 1.3 60.8 + - - +
75C ALA* 2.7 33.1 + - - +
78C LYS* 3.9 12.3 - - - -
79C ALA* 3.7 12.6 - - - -
293C LEU* 3.3 3.8 - - - -
294C VAL* 3.1 37.5 + - - +
309C LEU* 4.0 7.9 - - - -
400C HIS* 5.9 0.2 - - - -
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Residues in contact with ALA 47 (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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44C ILE* 4.6 1.1 - - + -
46C SER* 1.3 76.5 - - - +
48C THR* 1.3 63.0 + - - +
78C LYS* 5.9 0.4 - - - +
233C ASN 4.4 0.5 - - - +
234C GLU* 4.0 7.5 - - - +
292C ALA 3.5 7.2 - - - -
293C LEU* 3.8 13.0 - - + -
309C LEU* 4.7 0.4 - - - +
396C GLY* 3.6 33.2 - - - +
399C THR* 4.5 8.1 - - + -
400C HIS* 2.8 39.4 + - + +
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Residues in contact with THR 48 (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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47C ALA* 1.3 75.8 + - - +
49C ARG* 1.3 65.1 + - - +
71C ALA* 4.2 5.4 - - - +
74C GLY* 3.8 9.6 + - - -
75C ALA* 3.4 28.5 + - - +
78C LYS* 4.1 18.1 - - - +
234C GLU* 3.2 12.3 - - - +
236C ILE* 3.6 41.1 - - + -
291C ALA* 3.4 3.3 - - - +
292C ALA* 2.9 33.2 + - - +
293C LEU* 5.3 0.4 - - - +
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Residues in contact with ARG 49 (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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48C THR* 1.3 74.8 - - - +
50C THR* 1.3 83.8 + - - +
52C ILE* 3.9 9.5 - - - +
71C ALA* 4.6 3.1 - - - -
226C TRP* 4.4 0.2 - - - -
231C PHE* 4.0 16.0 - - - -
234C GLU* 2.9 43.6 + - + +
235C VAL* 3.4 23.7 - - + +
236C ILE* 2.9 32.2 + - - +
253C ASP* 2.9 42.6 + - - -
290C ALA 3.3 13.9 - - - +
291C ALA* 3.9 9.2 - - + +
383C LEU* 4.6 4.6 - - - +
389C MET* 4.4 3.4 - - + -
393C ARG* 3.6 36.6 - - - +
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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