Contacts of the strand formed by residues 52 - 60 (chain A) in PDB entry 1NB0
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 GLY 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER 3.7 0.6 + - - -
51A THR* 1.3 75.7 - - - +
53A ILE* 1.3 67.4 + - - -
54A TYR* 3.6 7.6 - - - -
71A SER* 3.6 1.9 - - - -
72A ILE 2.9 33.6 + - - +
109A TYR* 3.9 2.2 - - - -
111A ARG 3.2 12.6 - - - -
112A PRO 4.0 0.2 - - - -
113A GLU* 3.7 19.1 - - - +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY* 1.3 75.2 - - - -
54A TYR* 1.3 63.0 + - - +
69A VAL* 4.6 8.7 - - + -
70A VAL 3.5 4.7 - - - +
71A SER* 3.4 31.9 - - - +
109A TYR* 3.7 4.5 - - - -
110A LEU* 2.7 52.3 + - + +
111A ARG* 2.8 60.4 + - + +
113A GLU* 5.6 4.0 - - + -
129A ASP* 4.0 11.9 - - + +
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.1 19.7 - - + -
48A ASP 4.8 0.5 + - - -
49A ILE* 3.9 9.4 - - + -
50A SER* 2.7 48.3 + - - -
52A GLY 3.6 12.8 - - - -
53A ILE* 1.3 79.2 - - - +
55A TYR* 1.3 65.3 + - - +
69A VAL* 3.3 9.7 - - - +
70A VAL* 2.8 37.1 + - + +
72A ILE* 3.7 23.1 - - + -
106A ILE* 3.5 27.6 - - + -
108A GLY 3.1 20.4 - - - +
109A TYR* 3.3 28.0 - + + -
110A LEU* 4.2 1.3 - - - +
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR* 1.3 75.8 - - - +
56A GLY* 1.3 58.2 + - - +
68A MET* 3.4 12.1 - - - +
69A VAL* 4.3 0.7 - - + +
106A ILE* 3.8 2.0 - - - -
107A VAL* 2.8 37.3 + - + +
108A GLY* 2.9 35.7 + - - +
109A TYR 3.9 11.7 + - - -
110A LEU* 3.8 21.5 - - + -
133A ALA* 3.6 26.7 - - + -
136A ARG* 3.6 42.0 + - + -
137A LEU* 3.6 21.5 - - + -
142A TYR* 3.3 32.4 + + - -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 1.3 79.0 - - - +
57A TRP* 1.3 65.7 + - - -
67A LYS* 3.6 1.4 - - - -
68A MET* 3.0 34.6 + - - -
105A ALA 3.1 13.5 - - - -
107A VAL* 3.8 14.4 - - - -
137A LEU* 3.4 13.1 - - - +
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Residues in contact with TRP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY* 1.3 78.6 - - - -
58A ALA* 1.3 62.1 + - - +
65A VAL* 3.6 13.5 - - + -
66A HIS* 3.3 24.0 - - - -
67A LYS* 3.5 37.0 - - + -
68A MET* 3.6 3.9 - - - +
104A VAL* 3.4 2.8 - - - -
105A ALA* 2.9 31.8 + - + +
107A VAL* 4.0 7.4 - - + +
137A LEU* 3.6 34.3 - - + +
142A TYR 2.9 21.8 + - - -
143A LEU* 3.8 25.1 - - + -
145A ILE* 3.8 17.0 - - + -
146A LYS* 3.8 49.7 - - + +
151A PHE* 3.7 12.9 - - + -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TRP* 1.3 77.4 - - - +
59A SER* 1.3 59.9 + - - +
64A ASP 3.8 0.7 - - - +
65A VAL* 3.5 1.0 - - - +
66A HIS* 2.8 37.9 + - - +
68A MET* 3.6 22.0 - - + -
87A THR* 4.6 0.7 - - + -
89A ILE* 4.0 13.8 - - + +
102A LEU* 4.0 17.7 - - + -
103A ASN 3.1 11.0 - - - +
104A VAL* 4.2 4.7 - - + -
151A PHE* 4.2 4.3 - - - -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA* 1.3 75.2 - - - +
60A VAL* 1.3 63.9 + - - +
61A GLY 4.2 2.1 + - - -
63A GLY 3.7 13.4 + - - -
64A ASP 3.3 22.7 - - - -
65A VAL* 4.1 2.7 - - - -
66A HIS* 5.4 1.1 - - - -
89A ILE* 5.6 0.7 - - - -
102A LEU* 3.6 4.8 - - - +
103A ASN* 2.8 57.5 + - - +
151A PHE* 3.5 17.9 + - - +
154A SER* 4.5 2.8 + - - -
155A LYS* 5.8 0.7 - - - +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 1.3 76.7 - - - +
61A GLY* 1.3 60.4 + - - +
62A SER 3.1 0.3 + - - -
63A GLY* 2.8 31.5 + - - +
64A ASP 4.5 2.6 + - - -
66A HIS* 6.0 0.4 - - - -
89A ILE* 3.8 17.5 - - + -
93A PHE* 4.0 18.7 - - + -
97A PHE* 3.7 53.2 - - + -
100A GLU* 3.8 18.4 - - + +
101A ILE 3.6 4.9 - - - +
102A LEU* 4.2 6.1 - - + -
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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