Contacts of the strand formed by residues 62 - 68 (chain C) in PDB entry 1II4
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 LEU 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PRO* 3.1 5.7 - - - +
30C LYS 2.7 41.8 + - - +
32C LEU* 3.7 50.5 - - + +
41C LEU* 4.2 16.6 - - + +
43C ILE* 3.8 35.9 - - + -
59C HIS 4.7 0.2 - - - +
60C ILE* 3.3 16.6 - - - +
61C LYS* 1.3 74.4 - - - +
63C GLN* 1.3 60.7 - - - +
64C LEU* 4.1 6.8 + - + +
74C ILE* 4.1 15.5 - - + -
75C LYS 3.3 4.5 - - - +
76C GLY* 4.0 9.0 - - - -
77C VAL* 4.1 3.1 - - - -
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Residues in contact with GLN 63 (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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26C PHE 5.0 0.4 + - - -
27C LYS* 3.1 29.9 + - - +
28C ASP 4.3 3.4 + - - -
29C PRO* 3.8 19.1 - - - +
62C LEU* 1.3 74.0 - - - +
64C LEU* 1.3 84.8 + - - +
65C GLN* 3.9 6.5 + - + +
73C SER* 3.6 4.2 + - - +
75C LYS* 2.8 46.6 + - + +
77C VAL* 4.1 12.4 - - + +
321G ASP* 5.8 0.8 + - - -
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Residues in contact with LEU 64 (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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26C PHE 4.8 0.4 - - - +
28C ASP 5.4 2.2 + - - -
30C LYS* 5.5 17.5 - - + +
32C LEU* 4.6 11.9 - - + -
62C LEU* 4.2 11.8 + - + +
63C GLN* 1.3 97.4 + - - +
65C GLN* 1.3 62.6 + - - +
72C VAL* 4.3 12.3 - - + -
73C SER 3.4 4.5 - - - +
74C ILE* 3.9 25.1 - - + -
105C GLU* 3.7 22.4 - - - +
115C TYR* 3.8 22.9 - - + +
150C PRO* 6.3 1.8 - - + -
285G GLN* 3.5 33.8 + - + +
321G ASP* 4.8 1.4 - - - +
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Residues in contact with GLN 65 (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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63C GLN* 5.0 7.3 + - + +
64C LEU* 1.3 77.1 - - - +
66C ALA* 1.3 92.0 + - - +
67C GLU* 3.5 1.4 + - - +
72C VAL* 3.1 5.6 - - - +
73C SER* 2.9 43.7 + - - +
285G GLN* 4.4 1.1 - - - -
315G ALA* 3.8 2.4 - - - +
316G GLY 3.5 34.7 - - - +
317G VAL* 4.1 7.6 - - + +
320G THR* 3.8 8.6 - - - +
321G ASP* 3.1 48.8 + - - +
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Residues in contact with ALA 66 (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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65C GLN* 1.3 98.7 + - - +
67C GLU* 1.3 60.5 + - - +
68C GLU 4.0 1.8 - - - +
70C GLY 5.7 0.7 - - - +
71C VAL 3.1 13.2 - - - +
72C VAL* 4.0 4.5 - - + -
285G GLN* 4.0 14.8 - - + +
286G PRO 3.2 28.5 - - - +
287G HIS* 3.8 19.4 - - + -
315G ALA* 3.7 2.6 - - + -
316G GLY* 3.4 8.8 + - - -
321G ASP* 4.9 0.6 + - - -
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Residues in contact with GLU 67 (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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65C GLN* 3.5 4.1 + - - +
66C ALA* 1.3 75.6 - - - +
68C GLU* 1.3 63.9 + - + +
71C VAL* 2.8 13.6 + - + +
102C PHE* 3.4 40.0 - - + -
118C ARG* 5.3 6.3 - - - +
287G HIS* 3.5 5.2 + - - -
315G ALA 3.4 12.7 - - - +
316G GLY* 3.2 6.5 - - - -
317G VAL* 2.7 53.9 + - - +
318G ASN* 4.8 1.9 + - - +
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Residues in contact with GLU 68 (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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66C ALA* 3.4 2.2 - - - +
67C GLU* 1.3 78.2 - - - +
69C ARG* 1.3 69.4 + - + +
70C GLY 3.2 0.7 + - - -
71C VAL* 2.9 44.7 + - + +
104C PHE* 5.6 0.5 - - - -
118C ARG* 2.8 30.8 + - - +
287G HIS* 3.4 23.4 - - + +
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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