Contacts of the strand formed by residues 121 - 128 (chain D) in PDB entry 1NQ3
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 VAL 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN 4.2 0.3 - - - +
37D LEU* 3.4 22.2 - - - +
38D GLY 4.3 1.7 + - - -
51D VAL* 4.0 14.4 - - + +
54D GLU* 3.9 15.1 + - + +
55D ALA* 3.7 32.1 - - + +
58D ALA* 5.2 2.8 - - + +
81D VAL* 4.3 5.2 - - + -
82D LEU 3.4 13.5 - - - +
83D LEU* 4.0 13.9 - - + -
92D VAL* 4.5 9.2 - - + -
115D LEU* 3.4 4.4 - - - +
120D ARG* 1.3 83.8 + - - +
122D GLU* 1.3 63.9 + - - +
123D ILE* 4.1 21.5 - - + -
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Residues in contact with GLU 122 (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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35D GLY* 3.3 30.0 - - - +
36D GLN 3.4 12.8 - - - +
37D LEU* 3.5 18.1 - - + +
80D THR 3.7 0.9 - - - +
82D LEU* 2.9 47.4 + - + +
115D LEU* 3.5 27.7 - - + +
116D PRO* 3.6 18.6 - - - +
121D VAL* 1.3 74.0 - - - +
123D ILE* 1.3 67.7 + - - +
124D GLU* 4.3 0.4 - - + -
108F ALA* 4.2 17.0 - - - +
109F ALA 3.7 8.7 + - - +
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Residues in contact with ILE 123 (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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34D SER 4.1 0.9 - - - +
35D GLY* 3.6 0.8 - - - -
36D GLN* 2.8 33.4 + - - +
55D ALA* 4.9 3.4 - - - +
58D ALA* 4.6 10.3 - - + -
59D LEU* 3.8 35.4 - - + -
62D ILE* 3.6 30.0 - - + +
79D ALA* 4.8 10.8 - - + -
80D THR 3.4 10.1 - - - +
81D VAL* 4.4 19.3 - - + -
92D VAL* 5.1 6.3 - - + -
96D TYR* 4.7 6.3 - - + -
121D VAL* 4.1 17.9 - - + -
122D GLU* 1.3 81.0 - - - +
124D GLU* 1.3 67.1 + - - +
125D ALA* 5.2 0.7 - - + -
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Residues in contact with GLU 124 (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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33D ILE 4.0 7.0 - - - +
34D SER 4.5 0.4 - - - -
35D GLY* 3.8 21.1 - - - +
79D ALA* 3.4 3.1 - - - +
80D THR* 2.9 53.4 + - - +
82D LEU* 3.9 19.4 - - + +
122D GLU* 4.3 0.6 - - + -
123D ILE* 1.3 75.0 - - - +
125D ALA* 1.3 62.3 + - - +
78F LYS* 2.7 35.6 + - - +
80F THR* 4.6 2.8 + - - +
108F ALA* 3.8 17.7 - - - +
110F TYR* 4.2 7.1 + - - -
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Residues in contact with ALA 125 (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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33D ILE* 3.0 51.7 + - + +
62D ILE* 4.7 15.5 - - + +
76D VAL* 4.2 17.5 - - + -
78D LYS 3.3 11.2 - - - +
79D ALA* 4.5 5.8 - - + -
123D ILE* 4.3 0.6 + - + -
124D GLU* 1.3 77.5 - - - +
126D ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 126 (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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30D THR* 3.9 21.5 - - + -
31D ILE 3.3 9.4 - - - +
32D TYR* 4.2 25.6 - - + -
76D VAL* 3.5 5.7 - - - +
77D VAL* 3.0 36.6 + - + +
78D LYS* 2.9 27.3 + - + +
125D ALA* 1.3 80.5 - - - +
127D ALA* 1.3 63.6 + - - +
128D VAL* 5.4 0.4 - - + -
32E TYR* 4.0 30.3 - - + +
126E ILE* 6.0 2.0 - - + -
78F LYS* 5.9 5.6 - - - +
126F ILE* 5.9 2.9 - - + -
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Residues in contact with ALA 127 (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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30D THR* 3.6 3.1 - - - +
31D ILE* 2.6 51.4 + - + +
33D ILE* 4.7 2.7 - - + -
66D LEU* 3.7 29.6 - - + -
75D ASN* 3.3 21.8 - - + +
76D VAL* 4.1 3.1 - - + -
77D VAL 4.4 0.4 - - - +
125D ALA 4.3 0.2 - - - -
126D ILE* 1.3 74.8 - - - +
128D VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 128 (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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29D ARG* 3.3 12.8 - - + +
30D THR* 4.6 13.5 - - + +
71D CYS* 4.7 0.9 - - - -
75D ASN* 3.1 29.0 + - - +
77D VAL* 4.0 15.5 - - + -
126D ILE* 5.4 0.2 - - + -
127D ALA* 1.3 78.7 - - - +
129D GLN* 1.3 75.1 + - - +
132D LEU* 3.6 13.6 - - + +
4E LEU* 4.1 18.4 - - + -
27E VAL* 3.5 44.4 - - + -
32E TYR* 5.4 1.6 - - + +
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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