Contacts of the strand formed by residues 61 - 70 (chain A) in PDB entry 1W51
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A THR 4.5 1.2 + - - -
60A TYR* 1.3 83.5 - - - +
62A ASP* 1.3 68.8 + - - +
63A LEU* 4.1 4.6 - - + +
81A GLY* 3.1 1.7 - - - -
82A THR* 2.9 43.7 + - - +
96A ARG* 3.5 47.5 - - - +
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Residues in contact with ASP 62 (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 ARG* 5.7 2.2 + - - -
60A TYR* 3.3 30.3 + - + -
61A ARG* 1.3 79.7 - - - +
63A LEU* 1.3 80.2 + - - +
64A ARG* 2.8 38.7 + - - +
65A LYS 4.6 0.5 + - - +
79A GLU* 5.5 5.4 - - - +
80A LEU 3.4 7.5 + - - +
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Residues in contact with LEU 63 (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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61A ARG* 4.3 4.5 - - + +
62A ASP* 1.3 81.8 + - - +
64A ARG* 1.3 75.0 + - - +
65A LYS* 2.9 10.1 + - + +
80A LEU* 3.0 23.3 + - + +
81A GLY* 3.7 21.3 - - - +
82A THR* 3.8 28.7 - - + +
98A ASN* 4.5 5.8 - - - +
133A LEU* 5.1 9.9 - - + -
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Residues in contact with ARG 64 (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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62A ASP* 2.8 36.2 + - + +
63A LEU* 1.3 83.5 - - - +
65A LYS* 1.3 57.1 + - - +
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Residues in contact with LYS 65 (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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62A ASP* 4.6 0.5 + - - +
63A LEU* 2.9 9.5 + - + +
64A ARG* 1.3 79.0 - - - +
66A GLY* 1.3 66.2 + - - +
79A GLU* 3.7 3.7 - - - +
80A LEU* 2.8 53.3 + - + -
129A PRO* 4.1 14.8 - - + +
130A ASP* 4.1 17.8 + - - -
132A SER* 4.7 5.9 + - - -
133A LEU* 6.0 3.2 - - - +
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Residues in contact with GLY 66 (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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65A LYS* 1.3 86.9 - - - +
67A VAL* 1.3 63.2 + - - +
78A GLY 3.3 10.8 - - - -
79A GLU* 4.5 2.5 - - - -
80A LEU* 4.5 0.9 - - - +
129A PRO* 4.9 5.5 - - - +
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Residues in contact with VAL 67 (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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37A ASN* 4.7 1.6 - - - +
66A GLY* 1.3 71.9 - - - -
68A TYR* 1.3 74.2 - - - +
69A VAL* 4.0 6.5 - - + -
76A TRP* 4.1 7.5 - - + +
77A GLU* 3.3 6.8 - - - +
78A GLY 2.7 45.1 + - - +
80A LEU* 3.1 42.6 - - + -
100A ALA* 4.4 8.7 - - + -
128A ARG* 3.7 10.3 - - + +
129A PRO* 3.6 32.1 - - + -
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Residues in contact with TYR 68 (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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67A VAL* 1.3 76.2 - - - +
69A VAL* 1.3 65.7 + - - +
70A PRO* 3.2 43.0 - - + +
75A LYS* 3.8 32.6 - - + +
76A TRP 3.6 13.7 - - - -
77A GLU* 4.4 12.3 - - + +
128A ARG* 3.5 15.8 - - - +
129A PRO* 5.2 1.5 - - - +
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Residues in contact with VAL 69 (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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37A ASN* 3.9 10.1 - - + +
67A VAL* 4.0 3.1 + - + -
68A TYR* 1.3 79.8 - - - +
70A PRO* 1.3 62.5 - - + +
71A TYR* 3.4 38.4 + - + +
75A LYS* 3.6 2.5 - - - -
76A TRP* 2.9 73.3 + - + -
128A ARG* 3.5 26.2 - - + -
1506A L01 4.4 9.4 - - - -
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Residues in contact with PRO 70 (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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68A TYR* 3.2 45.5 - - + +
69A VAL* 1.3 84.6 - - - +
71A TYR* 1.3 65.4 + - - +
74A GLY 3.7 9.6 - - - +
75A LYS* 4.3 2.7 - - + -
128A ARG* 3.8 22.5 + - - +
1506A L01 3.4 20.4 - - - -
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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