Contacts of the strand formed by residues 36 - 44 (chain E) in PDB entry 1UW9
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 ILE 36 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E THR 3.8 10.1 - - - +
35E ASP* 1.3 71.9 - - - +
37E LEU* 1.3 67.1 + - - +
102E ALA* 3.5 1.7 - - - -
103E TYR* 2.8 41.3 + - + -
105E ILE* 4.2 8.7 - - - -
108E PHE* 3.6 38.1 - - + -
116E MET* 4.9 3.6 - - - -
120E ILE* 3.8 29.2 - - + -
138E LEU* 4.7 3.6 - - + -
139E ARG 3.5 10.5 - - - +
140E ILE* 4.9 7.6 - - + -
141E PRO* 3.7 24.0 - - + -
144E TYR* 4.2 22.9 - - + -
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Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 3.9 22.2 - - + -
35E ASP* 3.8 14.1 - - + -
36E ILE* 1.3 81.3 - - - +
38E ALA* 1.3 60.3 + - - +
85E TYR* 3.8 15.9 - - - +
101E VAL 3.3 2.5 - - - +
102E ALA* 3.8 23.1 - - + -
138E LEU* 3.1 10.6 - - - +
139E ARG* 2.7 72.9 + - + +
364E PHE* 3.7 25.1 - - + -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 1.3 76.0 - - - +
39E ALA* 1.3 59.8 + - - +
40E PHE* 3.6 26.9 - - + -
99E ALA 3.6 1.3 - - - +
100E TYR* 3.3 5.9 - - - -
101E VAL* 2.8 30.7 + - - +
103E TYR* 3.7 17.5 - - + -
120E ILE* 4.2 1.6 - - + -
135E LEU* 3.9 3.6 - - + -
137E ASP 3.5 4.5 - - - -
138E LEU* 3.7 16.6 - - + -
364E PHE* 3.7 5.5 - - - -
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA* 1.3 72.2 - - - +
40E PHE* 1.3 61.3 + - - +
98E ILE* 4.1 4.9 - - + -
99E ALA 3.7 3.1 - - - -
100E TYR* 3.9 10.5 - - + -
135E LEU* 3.7 2.6 - - - +
136E GLU* 2.9 30.5 + - + +
137E ASP 3.0 14.0 + - - +
363E TYR* 3.8 31.9 - - + -
364E PHE* 3.7 19.0 - - + -
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Residues in contact with PHE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA* 3.6 17.9 - - + -
39E ALA* 1.3 73.2 - - - +
41E ARG* 1.3 58.8 + - - +
42E MET* 3.5 1.1 + - + -
57E VAL* 3.7 22.0 - - + -
97E TYR 3.3 2.1 - - - +
98E ILE* 3.2 6.2 - - - -
99E ALA* 2.8 50.1 + - + +
101E VAL* 3.9 15.7 - - + -
103E TYR* 3.6 18.8 - - - -
120E ILE* 3.5 37.5 - - + -
124E VAL* 4.5 0.2 - - + -
125E PHE* 4.1 10.1 - + - -
133E LEU* 3.8 42.8 - - + -
134E ARG 3.4 1.8 - - - -
135E LEU* 4.0 20.2 - - + -
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Residues in contact with ARG 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA 4.0 1.2 + - - -
40E PHE* 1.3 69.2 - - - +
42E MET* 1.3 60.0 + - - +
43E THR* 5.4 0.4 - - - +
90E VAL* 3.8 13.3 - - + +
96E GLN* 3.1 43.5 + - + +
97E TYR 3.4 4.0 - - - +
98E ILE* 3.9 18.6 - - + +
132E ALA 4.1 0.2 - - - +
133E LEU* 3.3 6.2 - - - -
134E ARG* 2.7 46.1 + - + +
136E GLU* 2.8 34.9 + - + +
305E ARG* 3.2 49.9 + - - +
306E ASN* 4.3 7.7 - - - +
363E TYR* 3.6 15.1 + - - -
475E LEU* 3.2 23.6 + - - -
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Residues in contact with MET 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE* 4.2 5.6 - - - +
41E ARG* 1.3 72.8 - - - +
43E THR* 1.3 65.4 + - - +
44E PRO* 3.5 7.3 - - + +
50E PRO* 3.5 31.6 - - + +
53E CYS* 3.6 25.4 - - + +
54E GLY* 3.4 27.6 - - - -
57E VAL* 4.7 5.4 - - + -
87E ILE* 4.6 2.7 - - + -
96E GLN* 3.4 4.3 - - - -
97E TYR* 2.7 59.2 + - + +
99E ALA* 4.0 17.9 - - + -
130E LEU* 5.2 1.1 - - + -
132E ALA 3.9 0.7 - - - +
133E LEU* 3.9 19.3 - - + -
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Residues in contact with THR 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ARG* 5.1 0.7 + - - +
42E MET* 1.3 73.6 - - - +
44E PRO* 1.3 54.6 - - - +
95E ASN* 3.4 28.3 - - + +
96E GLN* 3.5 22.5 + - + +
130E LEU* 3.6 3.8 - - - -
131E ARG* 2.7 47.2 + - + +
132E ALA* 3.0 33.4 + - + +
306E ASN* 4.9 3.5 + - - +
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Residues in contact with PRO 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E MET* 3.5 10.9 - - + +
43E THR* 1.3 86.9 - - - +
45E GLN* 1.3 63.5 + - - +
48E VAL* 3.6 24.5 - - + +
50E PRO* 4.4 6.3 - - + -
53E CYS* 3.8 33.4 - - + -
95E ASN* 2.8 47.0 + - - +
97E TYR* 3.9 21.3 - - + -
129E ALA 4.0 0.7 - - - +
130E LEU* 4.3 0.2 - - - -
131E ARG* 3.9 4.5 - - - -
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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