Contacts of the strand formed by residues 34 - 41 (chain D) in PDB entry 1NUE
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 ARG 34 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 3.5 0.6 - - - +
32D GLY 4.0 1.1 + - - +
33D PHE* 1.3 73.2 - - - +
35D LEU* 1.3 67.1 + - - +
36D VAL* 3.4 15.2 + - - +
78D TRP* 3.3 5.6 - - - -
79D GLU* 2.8 82.5 + - - +
140D VAL 2.9 21.2 + - - -
141D ASP* 3.4 20.4 + - - +
142D TYR* 3.1 66.7 + - + +
143D LYS* 4.9 0.2 - - - +
144D SER* 3.8 24.9 - - - +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 5.7 2.2 - - + -
21A VAL* 5.0 15.5 - - + -
40A PHE* 3.5 27.6 - - + -
74A VAL* 5.1 0.4 - - + -
25D ILE* 5.5 1.6 - - + -
29D GLU* 6.2 0.4 - - + -
33D PHE 4.0 0.2 + - - -
34D ARG* 1.3 71.3 - - - +
36D VAL* 1.3 58.5 + - - +
37D ALA 3.5 23.1 - - - +
38D MET* 4.0 28.7 - - + -
76D MET* 4.2 7.9 - - + -
77D VAL 3.8 5.2 - - - +
78D TRP* 3.6 44.8 - - + +
142D TYR* 2.7 39.8 + - - +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.7 5.0 - - - -
6D ARG* 3.9 21.1 - - - +
34D ARG* 3.5 24.9 - - - +
35D LEU* 1.3 77.0 - - - +
37D ALA* 1.3 56.8 + - - +
77D VAL* 2.7 28.4 + - + +
78D TRP 4.4 1.3 - - - -
79D GLU* 3.5 27.1 - - + +
139D LEU* 3.9 22.0 - - + -
140D VAL* 2.8 51.6 + - - +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 4.0 8.0 - - - -
35D LEU* 3.5 7.3 - - - +
36D VAL* 1.3 81.7 - - - +
38D MET* 1.3 65.9 + - - +
76D MET* 3.2 2.9 - - - -
77D VAL* 2.9 29.3 + - + -
134D PHE* 3.7 15.7 - - + -
138D GLU 3.5 13.0 - - - +
139D LEU* 3.5 27.8 - - + -
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Residues in contact with MET 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.5 8.1 - - + -
38A MET* 3.8 25.1 - - + -
39A LYS* 3.3 2.6 - - - +
40A PHE* 3.1 40.0 + - + +
74A VAL* 3.7 33.7 - - + -
25D ILE* 3.8 24.2 - - + -
35D LEU* 4.0 23.6 - - + -
37D ALA* 1.3 78.9 - - - +
39D LYS* 1.3 67.3 + - - +
74D VAL* 4.0 7.9 - - + -
75D ALA 3.1 12.6 - - - +
76D MET* 3.8 16.2 - - + +
134D PHE* 3.8 4.1 - - - -
138D GLU 5.1 0.2 + - - -
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 3.3 11.0 - - - +
39A LYS* 4.8 5.4 - - + -
38D MET* 1.3 80.0 - - - +
40D PHE* 1.3 61.3 + - - +
41D LEU* 4.1 26.1 - - + +
73D VAL 3.9 0.3 - - - +
74D VAL* 3.5 3.4 - - - +
75D ALA* 2.8 36.0 + - + +
133D TRP* 2.8 27.5 + - - -
134D PHE* 3.7 22.2 - - + +
135D LYS* 4.8 4.8 - - - +
138D GLU* 2.7 36.5 + - - +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.3 36.8 - - + -
36A VAL 3.7 24.5 - - - -
37A ALA* 4.1 2.9 - - - -
38A MET* 3.1 30.3 + - + +
138A GLU* 4.5 7.4 - - - +
140A VAL* 3.8 20.0 - - + +
142A TYR* 3.6 20.9 - + - -
16D VAL* 4.0 15.7 - - + -
39D LYS* 1.3 75.5 - - - +
41D LEU* 1.3 64.7 + - - +
72D PRO* 3.5 34.3 - - + -
73D VAL 3.4 11.9 - - - -
74D VAL* 3.7 18.6 - - + -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.0 9.9 - - - -
39D LYS* 4.1 32.8 - - + +
40D PHE* 1.3 80.3 - - - +
42D ARG* 1.3 68.9 + - - +
43D ALA* 4.4 8.1 - - + +
47D HIS* 5.5 4.7 - - + +
72D PRO* 4.0 5.4 - - - -
73D VAL* 2.8 40.7 + - + +
75D ALA* 4.3 4.9 - - + -
133D TRP* 4.2 31.6 - - + -
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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