Contacts of the strand formed by residues 78 - 83 (chain D) 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 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D GLN* 4.1 2.0 - - - -
75D GLY* 2.7 37.7 + - - -
76D GLY 3.8 0.6 + - - -
77D MET* 1.3 83.0 + - - +
79D THR* 1.3 62.4 + - - +
80D VAL* 3.6 22.0 - - + -
91D PHE 3.3 13.5 - - - +
92D GLY* 3.9 3.4 - - - -
93D CYS 4.0 5.4 - - - +
98D ALA* 3.9 25.1 - - + +
99D LEU* 3.8 16.6 - - + -
126D ALA* 3.7 7.7 - - + +
127D GLY 3.1 27.3 + - - -
128D ASP 4.3 5.4 + - - -
130D HIS 3.6 10.8 - - - -
131D THR* 2.9 22.7 + - - -
410D HIS* 3.3 6.7 + - - -
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN 2.9 21.0 + - - -
73D GLU 3.4 13.2 - - - +
75D GLY 4.5 0.2 - - - +
78D HIS* 1.3 72.9 - - - +
80D VAL* 1.3 70.7 + - - +
81D CYS* 4.2 11.9 - - - -
90D SER* 3.2 5.4 - - - -
91D PHE* 2.7 65.0 + - + +
410D HIS* 2.9 17.0 + - - -
412D VAL* 3.6 22.7 - - + +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN 4.1 0.3 - - - +
72D ALA* 3.7 0.7 - - - -
73D GLU* 2.8 42.1 + - + +
78D HIS* 3.6 23.8 - - + +
79D THR* 1.3 80.3 - - - +
81D CYS* 1.3 62.9 + - - +
82D LEU 4.4 0.2 + - - -
88D VAL* 3.4 29.8 - - + -
89D TYR 3.3 4.0 - - - +
90D SER* 4.5 7.2 - - - -
98D ALA 5.1 0.4 - - - +
124D VAL* 4.2 20.1 - - + +
126D ALA* 4.3 9.0 - - + -
131D THR* 3.7 28.9 - - + +
143D TRP* 5.1 0.7 - - + -
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Residues in contact with CYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 3.9 29.6 - - - -
65D ILE* 3.9 20.6 - - + -
69D VAL* 4.0 11.4 - - + -
71D GLN 3.3 6.7 - - - +
72D ALA* 4.2 5.4 - - - -
79D THR* 4.2 7.4 - - - -
80D VAL* 1.3 81.6 - - - +
82D LEU* 1.3 60.8 + - - +
83D SER 4.1 0.2 + - - -
87D GLN 3.8 0.5 - - - +
88D VAL* 3.5 5.4 - - - +
89D TYR* 2.8 41.2 + - + +
91D PHE* 4.0 18.8 - - - -
124D VAL* 5.2 0.2 - - - -
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.2 6.4 - - - +
70D VAL* 2.8 39.9 + - + +
71D GLN* 2.8 26.4 + - + +
81D CYS* 1.3 72.6 - - - +
83D SER* 1.3 65.7 + - - +
86D GLY 3.9 5.8 - - - -
87D GLN 3.6 15.9 - - - +
88D VAL* 4.2 2.9 - - + +
121D VAL* 3.5 40.2 - - + +
122D VAL* 3.3 37.0 - - - +
123D GLN* 3.6 9.0 - - - +
124D VAL* 4.3 9.4 - - + +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLU* 3.1 27.0 + - - -
68D ASP 3.2 14.1 - - - -
69D VAL* 4.1 3.4 - - - +
70D VAL* 4.0 4.0 - - - +
81D CYS 4.1 0.8 + - - -
82D LEU* 1.3 79.9 - - - +
84D LYS* 1.3 59.2 + - - +
85D SER* 2.9 22.2 + - - -
86D GLY* 2.9 19.8 + - - -
87D GLN 2.9 25.5 + - - -
89D TYR* 4.0 9.1 - - - -
121D VAL 5.0 0.2 - - - +
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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