Contacts of the strand formed by residues 129 - 135 (chain A) in PDB entry 1NUS
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 GLU 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.1 41.0 - - + +
6A PRO 3.1 11.4 + - - +
7A VAL* 3.4 9.8 - - + +
8A VAL* 3.0 25.1 + - - +
39A TYR* 4.3 6.1 + - - -
101A HIS* 5.9 1.3 - - - -
104A LEU* 5.1 0.2 - - - -
127A VAL 5.1 3.1 - - - +
128A PRO* 1.3 72.1 - - - +
130A LEU* 1.3 59.5 + - - +
131A LYS* 3.1 31.3 + - - +
160A PHE 4.8 3.9 - - - +
188A ASN* 5.2 3.5 + - - -
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Residues in contact with LEU 130 (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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8A VAL* 3.4 39.0 - - + +
10A LEU* 4.1 13.9 - - + -
45A ILE* 5.1 1.6 - - + -
97A LEU* 3.3 47.1 - - + +
100A HIS* 3.7 15.5 - - + -
101A HIS* 3.7 22.3 + - + +
104A LEU* 4.2 14.8 - - + -
128A PRO 3.7 2.2 + - - -
129A GLU* 1.3 73.6 - - - +
131A LYS* 1.3 59.2 + - - +
160A PHE* 3.0 39.2 + - + +
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Residues in contact with LYS 131 (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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7A VAL* 4.4 20.0 - - + -
8A VAL 2.9 11.4 + - - +
9A LEU* 3.5 6.5 - - + +
10A LEU* 2.7 32.9 + - - +
33A LEU* 4.7 3.1 - - + -
39A TYR* 4.3 15.6 + - - -
97A LEU* 4.6 4.0 - - - -
129A GLU* 3.1 29.5 + - - +
130A LEU* 1.3 75.4 - - - +
132A LEU* 1.3 58.0 + - - +
133A LEU 3.5 0.3 + - - -
160A PHE 3.4 20.2 + - - +
161A GLY* 3.7 16.2 - - - +
163A VAL* 3.9 29.4 - - + -
188A ASN* 4.5 11.1 - - - +
190A HIS* 3.7 28.6 + - + -
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Residues in contact with LEU 132 (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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10A LEU* 3.4 15.3 - - + +
12A CYS* 4.5 17.5 - - + +
93A THR* 3.8 32.1 - - + -
97A LEU* 4.2 24.6 - - + +
131A LYS* 1.3 71.2 - - - +
133A LEU* 1.3 63.8 + - - +
134A CYS* 4.9 8.7 - - + -
138A VAL* 5.5 2.7 - - + -
142A PHE* 5.4 2.9 - - + -
148A TRP* 5.2 7.6 - - + -
156A ILE* 4.4 13.9 - - + -
161A GLY 3.0 15.2 + - - +
162A LEU* 3.5 26.2 - - + +
163A VAL* 2.9 23.7 + - - +
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Residues in contact with LEU 133 (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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9A LEU* 4.4 18.2 - - + -
10A LEU 2.8 18.5 + - - +
11A ALA* 3.6 18.9 - - + +
12A CYS 4.4 3.3 + - - +
25A MET* 3.8 24.6 - - + +
26A PHE* 3.5 60.3 - - + +
29A ALA* 3.5 26.0 - - + -
131A LYS 3.5 0.8 + - - -
132A LEU* 1.3 73.6 - - - +
134A CYS* 1.3 64.6 + - - +
163A VAL* 3.3 17.9 - - + +
165A VAL* 4.1 5.2 - - + -
501A APC 4.3 2.4 + - - -
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Residues in contact with CYS 134 (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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12A CYS 6.0 0.4 - - - +
25A MET* 4.0 9.1 - - - +
132A LEU* 4.9 6.3 - - + -
133A LEU* 1.3 77.0 - - - +
135A GLY* 1.3 69.4 + - - +
138A VAL* 3.9 26.7 - - + -
139A LEU* 4.8 6.7 - - - -
142A PHE* 6.0 0.2 - - - -
162A LEU* 4.0 25.8 - - - -
163A VAL 3.1 9.6 + - - +
164A CYS* 3.2 14.1 - - - -
165A VAL* 3.0 23.6 + - - +
501A APC 3.1 13.9 - - - +
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Residues in contact with GLY 135 (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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25A MET* 4.8 0.4 - - - -
134A CYS* 1.3 79.3 - - - +
136A ALA* 1.3 65.4 + - - -
137A ASP* 3.1 7.2 - - - -
138A VAL* 3.0 18.2 + - - +
139A LEU 3.7 1.0 + - - -
164A CYS* 4.0 1.3 - - - -
165A VAL* 3.5 9.4 - - - -
167A ARG* 4.2 0.9 - - - -
501A APC 3.0 40.5 + - - -
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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