Contacts of the helix formed by residues 37 - 53 (chain B) in PDB entry 1URV
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 ASN 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG 5.0 3.4 - - - +
34B LEU 3.3 7.6 + - - +
35B TYR 3.1 0.2 - - - -
36B ALA* 1.3 78.9 - - + +
38B SER* 1.3 64.6 + - - +
39B GLU* 3.1 7.5 + - - +
40B ASP* 3.2 43.4 + - - +
41B VAL* 3.2 24.5 + - + +
139B PHE* 5.9 2.2 - - + -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU 3.6 8.1 - - - -
35B TYR* 3.0 39.7 + - - +
36B ALA 3.5 0.4 - - - -
37B ASN* 1.3 75.9 - - - +
39B GLU* 1.3 71.8 + - - +
41B VAL 3.5 0.2 + - - -
42B GLY 3.0 23.9 + - - -
83B SER* 5.3 1.0 + - - -
86B MET* 3.3 36.0 - - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 4.9 2.3 - - - +
37B ASN* 3.1 4.8 + - - +
38B SER* 1.3 92.6 + - - +
40B ASP* 1.3 66.0 + - - +
42B GLY* 3.9 1.1 - - - -
43B VAL* 3.1 29.7 + - + +
79B ARG* 4.1 22.0 - - + +
82B ALA* 4.7 1.4 - - - +
83B SER* 4.2 23.1 - - - +
86B MET* 5.7 0.4 - - - -
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.2 35.9 + - - +
39B GLU* 1.3 75.2 - - - +
41B VAL* 1.3 60.8 + - - +
43B VAL* 3.5 6.0 + - - +
44B ALA* 3.0 28.8 + - - +
79B ARG* 3.9 17.3 + - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.7 25.6 - - + +
37B ASN* 3.2 26.1 + - + +
38B SER 3.8 2.9 - - - +
40B ASP* 1.3 74.6 - - - +
42B GLY* 1.3 60.5 + - - +
44B ALA* 3.2 6.4 + - - +
45B ILE* 2.9 44.0 + - + +
86B MET* 3.6 19.5 - - + -
134B VAL* 5.0 3.8 - - + +
135B VAL* 5.9 1.6 - - + -
138B GLU* 4.0 12.1 - - - +
139B PHE* 4.0 25.4 - - + -
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 3.0 12.0 + - - -
39B GLU 3.9 1.3 - - - -
41B VAL* 1.3 76.8 - - - +
43B VAL* 1.3 58.6 + - - +
45B ILE* 3.3 7.1 + - - +
46B LEU* 3.0 31.7 + - - +
82B ALA* 3.5 14.0 - - - +
85B VAL* 6.4 0.7 - - - -
86B MET* 3.7 28.5 - - - +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 3.1 19.3 + - - +
40B ASP* 3.9 5.4 - - - +
42B GLY* 1.3 72.9 - - - +
44B ALA* 1.3 67.3 + - - +
46B LEU* 3.9 0.3 - - - +
47B VAL* 3.0 25.3 + - + +
73B GLU* 3.7 40.6 - - + +
78B LEU* 3.7 17.3 - - + -
79B ARG* 4.2 30.3 - - + +
82B ALA* 3.9 16.2 - - + -
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Residues in contact with ALA 44 (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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40B ASP 3.0 19.7 + - - +
41B VAL* 3.5 5.4 - - - +
43B VAL* 1.3 79.3 - - - +
45B ILE* 1.3 62.2 + - - +
47B VAL* 4.1 4.9 - - - +
48B ARG* 3.2 24.4 + - - +
134B VAL* 4.4 8.0 - - + +
138B GLU* 3.7 22.7 - - - +
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Residues in contact with ILE 45 (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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34B LEU* 5.9 1.3 - - + -
41B VAL* 2.9 37.5 + - + +
42B GLY* 3.5 10.8 - - - +
44B ALA* 1.3 77.0 - - - +
46B LEU* 1.3 63.9 + - + +
48B ARG 3.4 0.2 + - - -
49B PHE* 3.0 26.3 + - - +
85B VAL* 6.2 2.9 - - + -
86B MET* 4.5 10.3 - - + -
89B LEU* 6.3 0.7 - - + -
127B LEU* 3.9 17.9 - - + -
130B VAL* 3.4 8.3 - - + +
131B ILE* 3.7 43.5 - - + +
134B VAL* 4.0 27.4 - - + -
135B VAL* 5.5 3.4 - - + -
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Residues in contact with LEU 46 (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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42B GLY 3.0 12.3 + - - +
43B VAL 4.0 2.9 - - - +
45B ILE* 1.3 84.5 - - + +
47B VAL* 1.3 63.1 + - - +
49B PHE* 3.3 8.0 + - + +
50B PHE* 2.9 52.5 + - + -
78B LEU* 3.5 20.2 - - + +
81B HIS* 3.7 28.0 - - + +
82B ALA* 3.2 43.7 - - + +
85B VAL* 4.7 9.9 - - + -
127B LEU* 4.4 15.0 - - + -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.0 28.7 + - + +
44B ALA* 4.1 4.9 - - - +
46B LEU* 1.3 76.8 - - - +
48B ARG* 1.3 59.1 + - - +
50B PHE* 3.8 0.3 - - - +
51B VAL* 2.9 41.1 + - + +
69B PRO* 3.9 30.7 - - + +
72B MET* 3.9 29.2 - - + -
73B GLU* 4.0 15.9 - - + +
78B LEU* 4.0 8.3 - - + -
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 2.9 25.3 + - - +
137A GLU* 5.0 2.7 + - - +
44B ALA 3.2 16.6 + - - +
45B ILE 3.6 4.3 - - - +
47B VAL* 1.3 79.3 - - - +
49B PHE* 1.3 55.8 + - - +
51B VAL* 3.9 4.2 - - - +
52B ASN* 2.9 64.5 + - - +
130B VAL* 3.7 18.8 - - + +
133B GLU* 3.6 5.7 - - - +
134B VAL* 4.2 15.2 - - + +
137B GLU* 2.9 41.0 + - - -
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE 3.0 17.8 + - - +
46B LEU* 3.5 9.4 - - + +
48B ARG* 1.3 76.1 - - - +
50B PHE* 1.3 79.6 + + - +
53B PHE* 2.8 37.8 + + + +
56B ALA* 3.5 28.0 - - + -
60B PHE* 5.7 0.2 - + - -
81B HIS* 6.2 1.8 - + - -
123B TYR* 4.1 14.8 - + - -
126B ILE* 3.8 16.2 - - + -
127B LEU* 3.7 52.9 - - + -
130B VAL* 3.7 18.3 - - + +
1172B HEM 3.7 27.4 - + + -
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Residues in contact with PHE 50 (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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46B LEU* 2.9 44.6 + - + +
47B VAL 3.9 2.5 - - - +
49B PHE* 1.3 94.3 - + - +
51B VAL* 1.3 64.1 + - - +
53B PHE 4.2 1.3 - - - -
54B PRO* 3.4 24.1 - - - +
56B ALA* 3.9 6.1 - - + -
57B LYS* 3.7 38.2 + - + +
60B PHE* 3.5 40.8 - + - -
63B PHE* 3.1 32.8 - + - -
72B MET* 4.2 10.3 - - - +
78B LEU* 3.9 15.7 - - + -
81B HIS* 5.3 0.4 - - - -
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Residues in contact with VAL 51 (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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132A LEU* 3.6 17.2 - - + +
47B VAL* 2.9 30.9 + - + +
48B ARG* 4.0 5.2 - - - +
50B PHE* 1.3 75.7 - - - +
52B ASN* 1.3 72.2 + - - +
54B PRO* 3.5 13.5 - - - +
67B GLU 5.2 1.1 - - - +
69B PRO* 4.2 17.3 - - + -
72B MET* 4.0 23.6 - - + -
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Residues in contact with ASN 52 (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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129A GLY* 3.7 15.8 + - - +
132A LEU* 3.6 23.2 - - - +
133A GLU* 3.4 27.7 + - - +
155A ARG* 2.6 34.0 + - - -
48B ARG* 2.9 46.6 + - - +
51B VAL* 1.3 83.2 - - - +
53B PHE* 1.3 75.1 + - + +
54B PRO* 3.5 0.7 - - - -
130B VAL* 5.5 1.8 - - + +
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Residues in contact with PHE 53 (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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53A PHE* 4.7 7.0 - + - -
125A LYS* 3.6 29.8 - - + -
126A ILE* 3.8 22.7 - - + -
129A GLY* 3.9 14.4 - - - -
130A VAL* 4.9 0.7 - - + -
155A ARG* 3.6 10.5 - - - -
1173A FC6 3.5 9.2 - - - +
49B PHE* 2.8 24.9 + + + +
50B PHE* 3.6 6.4 - - - +
52B ASN* 1.3 92.2 - - + +
54B PRO* 1.3 60.8 - - - +
55B SER* 3.1 5.2 - - - +
56B ALA* 2.8 36.3 + - + +
57B LYS 3.8 1.0 + - - -
123B TYR* 5.2 2.7 - - + -
126B ILE* 3.4 37.9 - - + -
130B VAL* 4.1 13.7 - - + -
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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
------------------------------------------------------------
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