Contacts of the strand formed by residues 102 - 107 (chain F) in PDB entry 5NSS
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 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F ARG* 3.3 18.8 - - - -
58F GLY 4.0 8.5 - - - -
59F PRO 4.2 7.2 - - - -
60F PHE* 5.0 0.4 - - - -
99F ALA 2.9 19.4 + - - +
100F ASP 3.2 1.0 + - - -
101F GLY* 1.3 78.3 - - - +
103F THR* 1.3 66.0 + - - -
104F LEU 3.8 0.2 + - - -
141F ASN 4.4 0.8 + - - -
142F VAL* 3.5 3.6 - - - -
143F ARG 3.5 14.6 + - - -
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Residues in contact with THR 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ALA 5.6 0.4 - - - -
50F HIS* 3.7 26.9 - - - +
55F ARG* 3.6 9.9 + - - +
60F PHE* 3.6 26.0 - - - +
61F ILE 3.8 5.7 + - - +
99F ALA* 4.9 2.0 - - - +
102F GLY* 1.3 74.8 - - - -
104F LEU* 1.3 62.9 + - - +
105F PHE* 4.1 0.8 + - - -
143F ARG* 3.7 21.1 - - - -
145F VAL* 5.7 4.7 - - - -
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Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ILE 4.1 5.6 - - - +
99F ALA* 4.2 20.9 - - + -
102F GLY 3.8 0.6 + - - -
103F THR* 1.3 72.0 - - - +
105F PHE* 1.3 59.9 + - - +
142F VAL* 4.5 7.6 - - + -
143F ARG 2.9 16.4 + - - +
144F LEU* 5.4 0.7 - - - -
145F VAL* 2.9 31.2 + - - +
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Residues in contact with PHE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ALA* 4.7 20.0 - - + -
61F ILE 3.8 7.8 + - - +
62F SER* 3.5 32.6 - - - +
63F LEU 3.6 4.0 + - - -
103F THR* 4.1 1.5 - - - -
104F LEU* 1.3 73.2 - - - +
106F LEU* 1.3 62.9 + - - +
107F ASP 3.8 0.9 + - - -
145F VAL* 3.5 15.0 - - + -
146F CYS 5.5 0.4 - - - +
147F ALA* 5.8 6.1 - - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LEU* 3.9 6.5 - - - +
105F PHE* 1.3 71.1 - - - +
107F ASP* 1.3 62.1 + - - +
108F GLU 3.6 0.3 + - - -
109F LEU* 4.3 18.6 + - + -
145F VAL 2.9 18.4 + - - +
146F CYS* 3.7 5.3 - - + -
147F ALA* 2.9 31.6 + - - +
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Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F SER* 5.7 4.5 - - - -
63F LEU 3.1 17.2 + - - +
64F ASN* 3.7 16.4 - - + +
65F CYS* 3.2 19.4 + - - +
105F PHE 3.8 2.9 + - - +
106F LEU* 1.3 69.5 - - - +
108F GLU* 1.3 73.3 + - + +
109F LEU* 4.6 0.2 - - - -
147F ALA* 4.2 6.3 - - - -
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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