Contacts of the strand formed by residues 39 - 48 (chain B) in PDB entry 1NUU
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 TYR 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.3 26.7 + - - -
5B ILE* 3.3 29.8 - - + +
7B VAL* 3.3 27.1 - - + -
33B LEU* 3.9 25.8 + - + +
34B HIS* 3.5 10.5 - - - -
36B THR* 3.4 18.6 - - + -
37B GLY 3.5 0.2 - - - -
38B MET* 1.3 100.3 - - + +
40B GLN* 1.3 62.3 + - - +
41B VAL 4.1 0.7 - - - +
129B GLU* 3.8 20.2 + - - -
131B LYS* 3.9 8.6 + - - -
187B HIS* 4.3 18.7 + - - -
188B ASN* 5.5 1.4 + - - -
190B HIS* 3.3 35.0 + + - -
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Residues in contact with GLN 40 (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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4B ARG* 4.0 22.0 - - + +
5B ILE 2.9 11.3 + - - +
6B PRO* 3.4 6.3 - - + +
7B VAL* 3.0 20.8 + - - -
34B HIS* 3.7 9.2 - - + +
39B TYR* 1.3 74.6 - - - +
41B VAL* 1.3 66.9 + - - +
42B ILE* 3.3 21.3 + - + +
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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
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7B VAL* 3.5 16.6 - - + +
9B LEU* 3.9 12.1 - - + -
30B ARG* 3.7 23.2 + - + -
33B LEU* 3.7 33.9 - - + -
34B HIS* 2.9 32.9 + - + +
40B GLN* 1.3 74.6 - - - +
42B ILE* 1.3 61.1 + - - +
43B GLN 4.1 4.3 - - - +
77B TRP* 3.5 34.9 - - + +
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Residues in contact with ILE 42 (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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6B PRO* 4.0 11.9 - - + -
7B VAL 2.8 20.1 + - - +
8B VAL* 4.0 10.1 - - + -
40B GLN* 3.6 34.3 - - + +
41B VAL* 1.3 75.2 - - - +
43B GLN* 1.3 73.4 + - + +
77B TRP* 4.5 10.1 - - - +
104B LEU* 6.2 0.2 - - + -
128B PRO* 3.7 34.1 - - + -
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Residues in contact with GLN 43 (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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7B VAL 3.6 1.1 + - - +
8B VAL* 3.3 20.4 - - + -
9B LEU 2.9 24.4 + - - -
41B VAL* 3.7 3.0 - - - +
42B ILE* 1.3 90.1 - - + +
44B GLY* 1.3 71.0 + - - +
45B ILE* 4.4 9.6 - - + -
76B ASP 5.3 0.3 - - - +
77B TRP* 3.3 34.2 - - - +
79B ARG* 3.2 34.2 - - - +
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Residues in contact with GLY 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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9B LEU 3.4 6.5 - - - -
26B PHE* 3.8 8.7 - - - -
43B GLN* 1.3 76.4 - - - +
45B ILE* 1.3 67.4 + - - +
77B TRP* 2.8 28.7 + - - +
78B ILE* 3.4 5.8 - - - -
79B ARG* 2.8 26.0 + - - +
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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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8B VAL* 3.7 25.8 - - + -
9B LEU 2.7 14.3 + - - +
10B LEU* 3.5 19.8 - - + +
11B ALA 2.8 31.4 + - - +
26B PHE* 3.7 3.3 - - - -
43B GLN* 4.4 3.8 - - + -
44B GLY* 1.3 79.1 - - - +
46B ILE* 1.3 66.9 + - - +
47B SER* 4.5 0.4 - - - +
79B ARG* 3.2 35.4 - - + +
81B ASP* 3.7 27.8 - - + -
100B HIS* 4.1 20.4 - - + +
104B LEU* 6.0 3.6 - - + -
130B LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 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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11B ALA 3.8 3.1 - - - -
15B PHE* 3.7 33.7 - - + -
18B ILE* 4.3 12.3 - - + -
23B LEU* 5.7 0.7 - - + -
26B PHE* 3.1 27.8 - - + -
45B ILE* 1.3 71.7 - - - +
47B SER* 1.3 61.3 + - - +
48B PRO* 3.3 10.1 - - + +
68B ALA* 4.1 17.5 - - + -
72B LEU* 3.8 14.4 - - + -
78B ILE* 3.0 35.2 - - + -
79B ARG 2.8 10.5 + - - +
80B VAL* 3.3 6.3 - - - -
81B ASP 2.9 24.9 + - - -
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Residues in contact with SER 47 (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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10B LEU* 3.9 23.6 - - - -
11B ALA 2.9 11.5 + - - -
12B CYS* 3.6 3.9 - - - -
13B GLY 3.5 17.7 + - - -
15B PHE* 4.0 2.5 - - - -
45B ILE* 3.7 3.1 + - - -
46B ILE* 1.3 73.8 - - - +
48B PRO* 1.3 64.8 - - - +
49B VAL 3.6 0.2 + - - -
81B ASP 3.8 9.2 + - - -
84B GLU* 2.5 45.3 + - - +
96B VAL* 4.0 4.2 - - - +
100B HIS* 4.5 3.9 + - - -
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Residues in contact with PRO 48 (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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13B GLY 3.4 7.9 - - - +
14B SER 4.4 1.3 - - - +
15B PHE* 3.8 15.3 - - + -
46B ILE* 3.3 14.4 - - + +
47B SER* 1.3 85.6 - - - +
49B VAL* 1.3 65.4 + - - +
61B SER 5.4 0.2 - - - +
64B ARG* 3.7 26.0 - - + +
65B VAL* 4.2 25.1 - - + -
68B ALA* 4.8 0.4 - - + -
80B VAL* 3.8 19.7 - - + -
81B ASP 3.9 7.6 - - - +
82B PRO* 5.2 0.4 - - + -
84B GLU* 3.9 4.2 - - - +
85B SER* 3.4 22.3 + - - +
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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