Contacts of the strand formed by residues 60 - 69 (chain A) in PDB entry 3S67
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLY* 1.3 74.8 - - - +
61A ASN* 1.3 76.5 + - - +
62A TYR* 3.7 32.4 + - + +
101A ILE 3.6 1.2 - - - +
102A TYR* 3.7 3.2 - - - -
103A ALA* 2.9 42.6 + - + +
105A PRO* 4.2 15.9 - - + -
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Residues in contact with ASN 61 (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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60A VAL* 1.3 83.1 - - - +
62A TYR* 1.3 64.7 + - - +
63A PHE* 3.5 31.3 - - + -
100A GLN* 3.9 22.0 + - - +
101A ILE 3.4 2.6 - - - +
102A TYR* 3.4 32.9 + - - +
124A IMD 5.1 6.0 - - - -
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Residues in contact with TYR 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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60A VAL* 3.7 34.3 - - + +
61A ASN* 1.3 77.7 - - - +
63A PHE* 1.3 62.3 + - - +
64A LEU* 4.1 17.3 - - + -
99A PHE 3.7 1.0 - - - +
100A GLN* 3.3 5.4 - - - +
101A ILE* 2.8 56.5 + - + +
103A ALA* 4.0 15.0 - - + -
105A PRO* 5.8 1.3 - - + +
110A MET* 6.0 2.9 - - - -
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Residues in contact with PHE 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 ASN* 3.5 39.9 - - + -
62A TYR* 1.3 74.4 - - - +
64A LEU* 1.3 67.6 + - - +
65A ASP* 4.2 5.1 + - - +
99A PHE 3.5 4.0 - - - -
100A GLN* 3.5 37.2 - - + -
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Residues in contact with LEU 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 TYR* 4.4 12.8 - - + -
63A PHE* 1.3 86.1 - - - +
65A ASP* 1.3 62.4 + - - +
66A VAL* 3.9 18.7 + - + +
97A CYS 3.6 1.4 - - - +
98A SER* 3.3 4.2 - - - -
99A PHE* 2.7 44.5 + - + +
101A ILE* 3.7 27.8 - - + -
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Residues in contact with ASP 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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63A PHE* 4.2 4.4 + - - +
64A LEU* 1.3 75.9 - - - +
66A VAL* 1.3 59.5 + - - +
96A PHE* 5.8 3.1 - - + -
97A CYS 3.4 3.5 - - - +
98A SER* 2.6 30.9 + - - -
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Residues in contact with VAL 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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64A LEU* 3.9 26.0 - - + -
65A ASP* 1.3 78.0 - - - +
67A GLU* 1.3 71.7 + - - +
68A LEU* 4.0 14.6 - - + -
95A ALA 3.8 0.3 - - - +
96A PHE* 3.4 6.7 - - - -
97A CYS* 2.7 41.0 + - - +
99A PHE* 4.0 23.8 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 1.3 83.7 - - - +
68A LEU* 1.3 69.6 + - - +
69A GLY 4.3 0.2 + - - -
94A LYS* 3.3 33.9 - - + +
95A ALA 3.3 12.1 - - - +
96A PHE* 3.6 42.7 - - + -
120A ALA* 4.0 1.4 - - - +
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Residues in contact with LEU 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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66A VAL* 4.0 19.7 - - + +
67A GLU* 1.3 80.9 - - - +
69A GLY* 1.3 61.5 + - - +
93A ARG 4.0 0.2 - - - +
94A LYS* 3.2 6.1 - - - +
95A ALA* 2.6 42.1 + - + +
97A CYS* 4.0 27.1 - - + -
99A PHE* 4.4 16.2 - - + -
117A CYS* 5.3 0.7 - - - -
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Residues in contact with GLY 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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67A GLU 4.3 0.2 + - - -
68A LEU* 1.3 77.7 - - - +
70A ARG* 1.3 65.1 + - - -
71A THR* 3.6 5.4 + - - +
85A PHE* 3.5 30.2 - - - -
93A ARG 3.4 7.4 - - - -
94A LYS* 4.4 9.4 - - - -
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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