Contacts of the strand formed by residues 45 - 51 (chain X) in PDB entry 1I9R
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 45 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37X VAL* 4.2 8.5 - - + -
38X LYS 3.6 1.1 - - - -
39X GLN* 3.1 42.4 - - + +
43X GLN* 5.7 0.2 + - - -
44X GLY* 1.3 73.3 - - - -
46X GLU* 1.3 63.7 + - - +
95X TYR* 5.2 4.0 - - + -
108X TRP* 4.8 0.4 - - + -
42Y GLN* 4.3 1.6 - - - +
48Y PRO* 4.4 15.7 - - + -
91Y TYR* 3.1 53.9 - - + -
102Y PHE* 3.5 56.5 + - + +
103Y GLY 5.5 1.2 + - - -
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Residues in contact with GLU 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X VAL* 3.0 7.5 - - - +
38X LYS* 2.7 58.7 + - + +
43X GLN* 4.6 22.0 - - + +
44X GLY 4.7 1.8 - - - +
45X LEU* 1.3 79.8 - - - +
47X TRP* 1.3 62.3 + - - +
48X ILE 3.6 0.2 + - - -
61X ASN* 5.0 3.6 + - - +
63X LYS* 4.2 18.1 + - - +
64X PHE* 3.2 34.2 - - + -
101Y THR* 6.5 0.2 - - - +
102Y PHE* 4.9 0.2 - - - -
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Residues in contact with TRP 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X TYR* 3.0 47.1 - + + -
36X TRP 3.7 7.6 - - - -
37X VAL* 4.5 4.0 - - + +
46X GLU* 1.3 71.6 - - - +
48X ILE* 1.3 61.8 + - - +
49X GLY* 3.0 23.3 + - - -
50X GLU* 3.3 16.4 - - + -
59X ASN 3.3 22.2 - - - -
60X PHE 3.7 2.5 - - - -
61X ASN* 3.1 52.8 + - + +
64X PHE* 4.3 2.3 - - - -
105X MET* 4.6 4.9 - - - -
98Y ILE* 3.9 22.0 - - + -
99Y PRO* 3.5 17.3 - - + -
100Y PRO* 3.2 49.9 + - + +
101Y THR* 5.9 0.8 - - - +
102Y PHE* 4.8 7.1 - - + -
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Residues in contact with ILE 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X TRP* 2.8 21.4 + - + +
37X VAL 4.1 2.0 - - - -
38X LYS* 3.7 21.5 - - + +
47X TRP* 1.3 74.8 - - - +
49X GLY* 1.3 56.3 + - - +
60X PHE* 3.5 5.9 - - + +
61X ASN* 2.6 37.1 + - - +
64X PHE* 3.7 34.2 - - + +
68X ALA* 3.6 30.7 - - + -
70X LEU* 5.2 1.8 - - + -
81X MET* 3.8 19.3 - - + -
83X LEU* 5.2 0.9 - - + -
94X TYR* 3.7 32.1 - - + -
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Residues in contact with GLY 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X TYR* 3.3 1.2 - - - -
36X TRP* 3.2 18.9 + - - +
47X TRP* 3.0 27.4 + - - -
48X ILE* 1.3 85.9 - - - +
50X GLU* 1.3 59.9 + - - -
59X ASN 3.1 12.3 - - - -
60X PHE* 3.9 3.1 - - - -
70X LEU* 3.7 13.5 - - - -
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Residues in contact with GLU 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X TYR* 3.4 13.0 - - + -
34X MET 3.5 6.3 - - - +
35X TYR* 3.9 20.4 + - + -
47X TRP* 3.4 9.5 - - + -
49X GLY* 1.3 76.0 - - - -
51X ILE* 1.3 61.1 + - - +
58X THR* 3.2 6.3 - - - -
59X ASN* 2.6 71.7 + - + +
70X LEU* 3.5 5.7 - - - +
102X ARG* 2.7 48.5 + - - -
98Y ILE* 3.4 7.1 - - - +
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Residues in contact with ILE 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X TYR* 3.6 4.7 - - - -
34X MET* 2.9 50.2 + - + +
36X TRP* 4.7 9.4 - - - +
50X GLU* 1.3 76.4 - - - +
52X ASN* 1.3 68.1 + - - +
53X PRO* 3.5 1.5 - - + -
56X GLY* 3.7 10.1 - - - +
57X ASP 3.3 9.4 - - - +
58X THR* 3.7 11.7 - - + -
70X LEU* 3.4 15.5 - - + +
71X THR* 3.4 33.2 - - - +
72X VAL* 3.4 33.0 - - + +
79X ALA* 4.8 2.7 - - + -
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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