Contacts of the strand formed by residues 410 - 416 (chain B) in PDB entry 1I2M
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 HIS 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B THR* 5.3 0.7 - - + -
40B LEU 3.3 14.1 - - - +
42B GLN 3.6 17.9 - - - +
47B GLN* 3.5 31.1 + - + +
48B LEU* 4.2 4.3 - - + -
74B ALA* 3.7 13.1 - - + +
75B GLY 3.4 25.4 - - - -
76B GLY 4.1 9.9 + - - -
78B HIS 3.4 11.5 + - - -
79B THR* 2.9 28.2 + - - -
376B GLN* 3.2 4.0 + - - +
406B SER* 3.1 2.6 + - - -
407B GLY* 2.8 27.0 + - - -
409B GLN* 1.3 79.1 + - - +
411B THR* 1.3 66.5 + - - +
412B VAL* 3.8 13.7 - - + -
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Residues in contact with THR 411 (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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39B THR* 3.3 5.2 - - - -
40B LEU* 2.9 53.4 + - + +
358B TYR* 2.5 41.6 + - + +
376B GLN* 3.6 5.6 - - - +
391B MET* 5.6 0.2 - - - -
404B VAL* 3.8 15.5 - - + -
405B SER 3.5 12.6 - - - +
406B SER* 2.9 14.8 + - - +
410B HIS* 1.3 72.5 + - - +
412B VAL* 1.3 71.5 + - - +
413B LEU* 4.7 2.9 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.7 20.4 - - + -
38B LEU 3.4 3.6 - - - +
39B THR* 4.0 6.7 - - + -
72B ALA* 3.6 35.0 - - + +
74B ALA* 3.9 11.9 - - + -
79B THR* 3.6 35.4 - - + +
403B SER* 4.2 0.3 + - - +
404B VAL* 3.5 4.0 - - - +
405B SER* 2.7 37.8 + - - +
410B HIS* 3.8 11.4 - - + -
411B THR* 1.3 79.2 - - - +
413B LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 413 (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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36B LEU 3.6 0.3 - - - +
37B VAL* 3.5 7.1 - - - +
38B LEU* 2.8 45.9 + - + +
40B LEU* 4.4 9.6 - - + -
60B PRO* 4.0 20.4 - - + -
72B ALA* 4.9 1.6 - - - -
366B VAL* 4.3 12.3 - - + -
391B MET* 3.9 27.1 - - + -
396B LEU* 4.4 15.9 - - + -
401B VAL* 4.3 10.8 - - + -
403B SER 3.5 5.6 - - - +
404B VAL* 3.5 34.8 - - + -
411B THR* 4.7 1.1 - - + -
412B VAL* 1.3 76.7 - - - +
414B LEU* 1.3 60.0 + - - +
415B VAL* 4.0 8.7 - - + -
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Residues in contact with LEU 414 (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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33B GLU 4.1 9.2 - - - +
35B GLY 3.8 9.6 - - - -
36B LEU 3.4 15.9 - - - +
37B VAL* 4.1 4.3 - - + -
69B VAL* 3.6 35.0 - - + +
70B VAL 3.4 33.2 - - - +
71B GLN* 4.0 3.1 - - - +
72B ALA* 4.5 7.8 - - + +
401B VAL 3.7 0.3 - - - -
402B LEU* 2.7 48.4 + - + -
403B SER* 3.1 31.8 + - - +
413B LEU* 1.3 73.7 - - - +
415B VAL* 1.3 55.8 + - - +
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Residues in contact with VAL 415 (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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35B GLY* 3.1 6.4 - - - -
36B LEU* 2.7 55.7 + - + +
38B LEU* 3.8 32.8 - - + -
396B LEU* 4.1 16.8 - - + -
399B ARG* 3.8 27.6 - - + -
400B VAL 3.3 13.5 - - - +
401B VAL* 4.2 8.7 - - + -
402B LEU* 4.2 2.9 - - - +
413B LEU* 4.3 7.0 - - + -
414B LEU* 1.3 78.2 - - - +
416B LYS* 1.3 61.5 + - - +
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Residues in contact with LYS 416 (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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33B GLU* 2.7 33.0 + - - +
34B PRO* 4.1 14.6 - - - +
35B GLY* 4.8 1.1 - - - -
36B LEU* 5.7 3.4 - - - -
399B ARG* 2.9 9.7 - - - -
400B VAL* 2.7 44.2 + - + +
402B LEU* 3.9 21.8 - - + +
415B VAL* 1.3 74.9 - - - +
417B ASP* 1.3 74.7 + - + +
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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