Contacts of the strand formed by residues 110 - 117 (chain B) in PDB entry 5E0T
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 LYS 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B CYS 5.5 2.6 + - - -
86B ASP* 6.0 2.0 - - - -
103B PHE 4.7 0.4 - - - +
104B GLU* 4.0 0.3 - - - +
105B ALA* 3.1 41.9 + - + +
107B ASN 4.2 1.8 + - - -
108B GLN* 3.1 3.0 - - - +
109B GLU* 1.3 81.8 - - + +
111B VAL* 1.3 69.7 + - - +
112B SER* 4.0 10.5 - - - +
143C GLU* 3.9 26.1 - - - +
146C ARG* 4.3 22.6 - - - +
147C ILE* 4.5 11.5 - - - +
150C ASP* 4.7 5.9 + - - -
180C ILE* 3.7 24.2 - - + +
181C LYS 3.6 2.5 - - - -
182C LEU* 3.6 18.4 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 4.1 20.4 - - + -
103B PHE 3.5 8.7 - - - +
104B GLU* 4.3 12.3 - - + -
108B GLN* 4.6 25.4 - - + +
109B GLU 5.3 0.4 - - - -
110B LYS* 1.3 81.5 - - - +
112B SER* 1.3 67.0 + - - +
113B ASP* 5.5 2.9 - - + +
179C ASN 3.9 0.9 - - - +
180C ILE* 3.6 0.7 - - - -
181C LYS* 2.9 43.6 + - + +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B CYS 5.0 3.3 + - - -
102B VAL* 3.3 7.6 - - - +
103B PHE* 2.7 47.0 + - - +
110B LYS* 4.0 11.1 - - - -
111B VAL* 1.3 75.5 - - - +
113B ASP* 1.3 63.4 + - - +
114B TYR* 3.6 24.4 + - - -
179C ASN 3.3 7.4 - - - -
180C ILE* 3.5 22.7 - - - +
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA* 5.0 1.6 - - - +
101B LEU 3.5 5.5 - - - +
102B VAL* 4.4 14.6 - - + +
111B VAL* 5.5 3.4 - - + +
112B SER* 1.3 77.5 - - - +
114B TYR* 1.3 64.1 + - - +
115B GLU* 3.1 30.1 - - - +
178C GLY* 3.2 2.8 - - - -
179C ASN* 2.9 57.7 + - - +
181C LYS* 5.7 3.4 - - - -
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.7 27.4 - - + -
81B CYS* 3.3 26.7 + - + +
100B ALA* 3.3 5.4 - - - -
101B LEU* 2.8 39.4 + - + +
103B PHE* 3.5 35.7 - + - -
112B SER* 3.6 19.3 - - - -
113B ASP* 1.3 76.0 + - - +
115B GLU* 1.3 68.5 + - - +
116B MET 4.0 0.4 - - - -
150C ASP* 4.3 1.4 + - - +
151C LEU* 4.1 7.8 - - + +
154C ILE* 4.0 31.2 - - + -
177C ASN 3.4 3.8 - - - -
178C GLY* 3.6 22.9 - - - -
179C ASN 5.1 0.4 - - - -
180C ILE* 3.8 24.1 - - + +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.8 3.2 - - - +
98B THR* 4.6 18.6 - - + +
99B LEU 3.7 2.9 - - - -
100B ALA* 3.6 16.9 - - + +
113B ASP* 3.1 32.9 - - - +
114B TYR* 1.3 76.9 - - - +
116B MET* 1.3 60.6 + - - +
117B LYS* 5.4 0.2 - - - +
175C LEU* 5.2 0.2 - - - +
176C GLY* 3.3 8.0 - - - -
177C ASN* 2.8 55.1 + - - +
179C ASN* 5.2 2.3 + - - -
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 4.1 19.5 - - + -
71B ASN 4.4 2.7 - - - +
74B SER* 4.3 8.1 - - - -
75B MET* 3.5 52.7 - - + -
78B ILE* 3.5 21.3 - - + -
98B THR* 3.1 7.0 - - - -
99B LEU* 2.8 72.6 + - + +
101B LEU* 4.2 4.5 - - + -
114B TYR 4.0 0.8 - - - -
115B GLU* 1.3 72.9 - - - +
117B LYS* 1.3 73.8 + - - +
118B LEU* 4.4 1.7 - - + +
175C LEU 4.0 7.0 - - - +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 5.7 0.3 - - - -
71B ASN* 5.3 8.0 + - - +
74B SER* 5.8 0.9 - - - -
97B ASP 4.1 4.7 - - - +
98B THR* 4.4 11.4 - - + -
115B GLU 3.9 1.0 + - - +
116B MET* 1.3 83.2 - - - +
118B LEU* 1.3 64.9 + - - +
119B MET* 4.2 0.7 + - - +
173C GLY 4.1 4.6 + - - -
174C GLU* 2.8 56.8 + - - +
175C LEU* 3.1 17.4 + - - +
176C GLY* 4.3 10.5 - - - +
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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