Contacts of the strand formed by residues 98 - 104 (chain E) in PDB entry 6S1M
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 THR 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E ARG 4.8 0.2 - - - +
92E ALA* 4.4 12.5 - - - +
93E GLU 4.5 0.3 + - - -
96E ALA* 3.1 30.8 + - + +
97E ASP* 1.3 82.0 - - - +
99E LEU* 1.3 66.7 + - - +
100E ALA* 4.3 0.7 + - - +
115E GLU* 4.2 19.7 + - - +
116E MET 3.3 15.4 + - - -
117E LYS* 4.6 4.0 - - - -
118E LEU* 3.5 9.3 - - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E PHE* 4.7 0.7 - - + -
28E TRP* 6.5 1.1 - - + -
68E MET* 3.9 22.9 - - + -
70E VAL* 5.1 4.5 - - + -
75E MET* 4.9 11.7 - - + -
90E LEU* 4.5 17.5 - - + -
91E ARG 3.4 28.5 - - - +
92E ALA* 3.8 10.8 - - + -
98E THR* 1.3 76.1 - - - +
100E ALA* 1.3 70.8 + - - +
101E LEU* 4.1 9.8 + - + -
114E TYR 3.7 0.2 - - - +
115E GLU* 3.4 1.7 - - - -
116E MET* 2.7 61.8 + - + +
118E LEU* 3.8 17.5 - - + +
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Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR 3.1 6.1 - - - +
90E LEU* 3.5 3.6 - - - -
91E ARG* 2.9 57.2 + - + +
98E THR 5.7 0.2 - - - +
99E LEU* 1.3 76.1 - - - +
101E LEU* 1.3 63.1 + - - +
102E VAL* 4.0 0.9 - - + -
113E ASP* 4.5 4.0 - - - +
114E TYR 3.2 3.8 - - - -
115E GLU* 3.6 26.9 - - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E MET* 4.7 9.6 - - + -
78E ILE* 4.0 13.5 - - + -
79E LEU* 3.7 35.2 - - + -
88E ILE* 5.2 0.4 - - + -
89E THR 3.6 3.8 - - - -
90E LEU* 4.3 19.5 - - + -
99E LEU* 4.3 9.0 - - + +
100E ALA* 1.3 75.7 - - - +
102E VAL* 1.3 60.6 + - - +
103E PHE* 3.9 19.7 - - + -
113E ASP* 3.5 1.2 - - - -
114E TYR* 2.5 54.4 + - + +
116E MET* 4.2 36.1 - - + -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ILE 3.4 4.0 - - - +
88E ILE* 3.5 1.0 - - - -
89E THR* 2.9 46.1 + - + +
91E ARG* 3.7 28.7 - - + +
100E ALA 5.0 2.2 - - - -
101E LEU* 1.3 74.5 - - - +
103E PHE* 1.3 65.6 + - - +
104E GLU* 4.5 13.0 - - + +
111E VAL* 3.7 21.3 - - + -
112E SER 3.2 10.5 - - - +
113E ASP* 3.3 24.9 - - + +
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Residues in contact with PHE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 3.9 13.5 - - + -
79E LEU* 4.0 9.9 - - + -
81E CYS 3.6 19.5 - - - -
82E ALA* 3.7 19.3 - - + -
86E ASP* 4.1 18.4 - - + +
87E ILE 3.3 2.5 - - - -
88E ILE* 3.5 37.0 - - + -
101E LEU* 3.9 33.0 - - + -
102E VAL* 1.3 80.2 - - - +
104E GLU* 1.3 61.5 - - - +
105E ALA 4.0 0.7 + - - -
110E LYS 4.7 0.2 - - - -
111E VAL* 3.4 4.9 - - - +
112E SER* 2.8 42.4 + - - +
114E TYR* 3.7 30.7 - + - -
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.3 37.8 + - - -
86E ASP* 3.1 4.5 - - - -
87E ILE* 2.7 52.4 + - + +
89E THR* 4.1 7.8 + - - -
102E VAL* 4.5 8.6 - - + +
103E PHE* 1.3 77.0 - - - +
105E ALA* 1.3 68.4 + - - +
106E PRO 3.6 0.5 - - - -
108E GLN* 6.0 3.2 - - + +
110E LYS 4.1 3.8 - - - +
111E VAL* 4.4 20.9 - - + -
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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