Contacts of the helix formed by residues 25 - 34 (chain B) in PDB entry 1NUA
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PRO* 4.1 24.7 - - + -
6B LYS* 3.3 30.2 + - - -
16B ILE* 3.7 23.1 - - + +
21B LEU* 2.9 37.0 + - + +
23B ARG 3.8 1.0 - - - -
24B ASN* 1.3 77.3 - - + +
26B VAL* 1.3 59.5 + - - +
27B ALA 3.6 1.7 - - - +
28B LYS* 3.5 23.7 + - - +
29B ASP* 2.8 62.6 + - + -
174B TYR* 3.8 7.9 - + - -
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Residues in contact with VAL 26 (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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21B LEU* 2.9 32.0 + - + +
22B TRP* 3.7 26.0 - - + +
25B TYR* 1.3 73.5 - - - +
27B ALA* 1.3 67.5 + - - +
29B ASP* 3.0 4.5 + - - +
30B LEU* 2.9 34.7 + - + +
55B PHE* 3.5 24.9 - - + -
110B ILE* 5.6 1.1 - - + -
137B VAL* 5.1 2.0 - - + -
174B TYR* 3.9 42.2 - - + -
176B ASP* 6.2 0.2 - - + -
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Residues in contact with ALA 27 (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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22B TRP 5.2 0.4 + - - -
25B TYR 3.6 0.8 - - - +
26B VAL* 1.3 79.3 - - - +
28B LYS* 1.3 62.7 + - - +
30B LEU* 3.5 3.3 + - - +
31B ILE* 3.0 29.4 + - - +
55B PHE* 3.4 28.0 - - + -
58B ALA* 3.3 38.6 - - + +
59B PHE* 4.0 10.3 - - + -
62B ARG* 4.7 2.0 - - + -
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Residues in contact with LYS 28 (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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24B ASN 4.9 7.6 - - - +
25B TYR* 3.5 34.6 + - - +
26B VAL 3.2 0.4 - - - -
27B ALA* 1.3 78.9 - - - +
29B ASP* 1.3 102.8 + - - +
31B ILE* 3.3 7.3 + - - +
32B SER* 3.2 29.3 + - - +
62B ARG* 3.7 49.0 - - + +
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Residues in contact with ASP 29 (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 LYS* 5.2 1.0 + - - -
16B ILE* 3.9 0.2 - - - +
25B TYR* 2.8 55.7 + - + +
26B VAL 3.6 0.9 - - - +
28B LYS* 1.3 86.3 + - - +
30B LEU* 1.3 59.1 + - - +
32B SER* 3.2 3.0 + - - -
33B ASP* 2.8 42.2 + - - +
172B LYS* 2.9 26.9 + - - -
174B TYR* 2.6 26.9 + - - +
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Residues in contact with LEU 30 (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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26B VAL* 2.9 32.7 + - + +
27B ALA* 3.7 7.9 - - - +
29B ASP* 1.3 74.2 - - - +
31B ILE* 1.3 59.9 + - + +
34B CYS* 2.6 51.1 + - + -
39B TYR* 3.5 22.0 - - + -
55B PHE* 4.4 12.3 - - + -
59B PHE* 5.7 1.8 - - + -
108B VAL* 4.4 4.3 - - + -
110B ILE* 3.3 31.9 - - + -
135B VAL* 3.9 30.7 - - + -
174B TYR* 4.1 10.1 - - + +
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Residues in contact with ILE 31 (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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27B ALA 3.0 19.3 - - - +
28B LYS* 3.3 9.3 + - - +
30B LEU* 1.3 79.9 - - + +
32B SER* 1.3 66.4 + - - +
35B SER* 3.5 20.6 + - - -
39B TYR* 3.4 15.9 - - + +
59B PHE* 3.6 30.1 - - + -
62B ARG 4.5 16.8 - - - +
63B ALA* 4.6 4.3 - - + +
66B ILE* 4.0 34.3 - - + -
70B PRO* 4.0 19.1 - - + -
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Residues in contact with SER 32 (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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28B LYS* 3.2 20.8 + - - -
29B ASP* 3.3 13.5 + - - -
31B ILE* 1.3 83.8 - - - +
33B ASP* 1.3 72.8 + - - +
35B SER* 4.9 3.1 + - - -
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Residues in contact with ASP 33 (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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12B ARG* 3.8 11.2 + - - +
29B ASP* 2.8 24.2 + - - +
32B SER* 1.3 87.0 + - - +
34B CYS* 1.3 65.7 + - - +
35B SER 3.6 2.5 + - - -
133B ARG* 5.1 1.4 + - - -
171B THR* 5.4 1.7 - - - +
172B LYS* 3.3 35.3 + - - -
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Residues in contact with CYS 34 (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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30B LEU* 2.6 39.0 + - + +
33B ASP* 1.3 79.1 - - - +
35B SER* 1.3 62.5 + - - +
36B SER* 3.6 2.3 - - - -
39B TYR* 2.5 24.8 + - - +
108B VAL* 3.8 17.8 - - + +
133B ARG* 3.9 10.3 - - - +
135B VAL* 4.5 3.6 - - - -
171B THR* 3.6 32.3 - - - -
172B LYS* 4.0 19.3 - - - -
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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