Contacts of the strand formed by residues 42 - 49 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS 4.1 0.7 - - - +
41B GLU* 1.3 80.0 - - - +
43B VAL* 1.3 71.9 + - - +
137B SER* 3.8 40.6 - - - +
140B LEU* 3.8 36.3 - - + -
141B MET* 3.8 17.3 - - + +
295B LEU* 4.6 2.9 - - + -
296B MET 3.5 3.6 - - - +
311B ARG* 3.7 5.0 - - - +
312B ILE* 2.9 48.7 + - + +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.9 21.3 - - - +
42B VAL* 1.3 81.5 - - - +
44B ILE* 1.3 62.3 + - - +
45B VAL* 3.8 10.5 + - + -
295B LEU* 3.4 6.4 - - - +
296B MET* 2.8 51.5 + - + +
297B THR 4.3 3.4 - - - +
298B ALA* 4.7 8.1 - - + -
301B ALA* 4.3 8.1 - - + -
308B PRO* 3.7 31.4 - - + -
310B ALA 3.3 12.3 - - - +
311B ARG* 4.3 2.5 - - - +
312B ILE* 5.1 0.2 - - - -
427B LEU* 4.3 10.1 - - + -
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 1.3 71.4 - - - +
45B VAL* 1.3 61.2 + - - +
46B SER 3.6 20.4 - - - +
47B ALA* 4.5 0.2 - - + -
293B LEU* 4.0 13.0 - - + -
294B VAL 3.7 5.6 - - - +
295B LEU* 3.8 19.1 - - + -
308B PRO* 3.7 1.8 - - - +
309B LEU* 2.8 24.6 + - - +
310B ALA* 2.8 24.1 + - + +
312B ILE* 3.7 25.8 - - + -
395B VAL* 4.2 12.6 - - + -
399B THR* 3.6 37.7 - - + +
424B ILE* 4.0 17.3 - - + -
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 4.2 15.0 - - + +
44B ILE* 1.3 76.2 - - - +
46B SER* 1.3 60.4 + - - +
78B LYS 5.2 1.0 - - - +
79B ALA* 3.8 29.8 - - + +
294B VAL* 2.9 13.1 + - + +
296B MET* 3.7 33.9 - - + -
301B ALA* 4.8 0.4 - - + -
306B VAL* 3.3 37.0 - - + -
307B THR 4.7 3.3 - - - +
308B PRO* 4.2 5.2 - - + -
309B LEU* 3.6 19.5 + - - +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.6 9.1 - - - +
45B VAL* 1.3 79.4 - - - +
47B ALA* 1.3 63.2 + - - +
75B ALA* 2.6 31.2 + - - -
78B LYS* 4.0 12.8 - - - -
79B ALA* 3.7 13.5 - - - +
292B ALA 4.7 0.2 - - - -
293B LEU* 3.3 2.9 - - - -
294B VAL* 3.1 37.3 + - - +
309B LEU* 4.0 8.5 - - - -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 4.5 0.2 - - + -
46B SER* 1.3 79.4 - - - +
48B THR* 1.3 62.5 + - - +
78B LYS* 5.6 0.2 - - - +
233B ASN 4.1 3.6 - - - +
234B GLU* 4.1 2.9 - - - +
292B ALA 3.5 7.2 - - - -
293B LEU* 3.7 13.9 - - + -
309B LEU* 4.5 0.8 - - - +
396B GLY* 3.6 31.9 - - - +
399B THR* 4.5 9.0 - - + -
400B HIS* 2.7 40.4 + - + +
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA* 1.3 77.1 + - - +
49B ARG* 1.3 65.2 + - - +
71B ALA* 4.1 6.7 - - - +
74B GLY* 4.0 8.3 - - - +
75B ALA* 3.4 27.0 + - - +
78B LYS* 3.7 18.9 + - - +
233B ASN 4.9 0.7 + - - -
234B GLU* 3.4 9.4 + - - +
236B ILE* 3.6 44.9 - - + -
291B ALA* 3.3 2.6 - - - +
292B ALA* 2.8 32.8 + - - -
293B LEU* 5.4 0.2 - - - +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B THR* 1.3 78.6 - - - +
50B THR* 1.3 84.5 + - - +
52B ILE* 3.9 10.1 - - - +
71B ALA* 4.5 2.5 - - - -
231B PHE* 4.0 15.8 - - - -
234B GLU* 2.9 37.2 + - + +
235B VAL* 3.3 28.8 - - + +
236B ILE* 2.9 31.6 + - - +
253B ASP* 2.9 41.6 + - - -
290B ALA 3.3 14.4 - - - +
291B ALA* 3.8 8.3 - - + -
383B LEU* 4.6 4.9 - - - +
389B MET* 4.0 4.0 - - + -
393B ARG* 3.7 36.0 - - - +
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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