Contacts of the strand formed by residues 103 - 112 (chain J) in PDB entry 6C6S
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 103 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J ILE 5.2 0.5 - - - +
33J TRP* 5.9 0.5 - - - +
34J SER* 3.3 15.8 - - - -
35J PHE 4.0 1.8 - - - -
36J GLY 4.1 6.1 - - - -
61J ILE* 4.5 0.9 - - - -
62J PHE* 3.7 7.4 - - - -
102J MET* 1.3 77.3 - - - +
104J HIS* 1.3 64.1 + - - +
243J PRO* 3.6 7.1 - - - +
244J VAL* 3.2 36.4 + - - +
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Residues in contact with HIS 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE* 4.4 7.0 - - + -
31J ARG* 5.0 9.5 - - + +
34J SER* 2.6 31.0 + - - +
36J GLY* 3.6 7.3 + - - -
37J GLU* 3.3 35.2 + - + +
38J VAL* 3.0 27.4 + - - +
103J GLY* 1.3 75.1 - - - +
105J ILE* 1.3 66.5 + - - +
106J GLU* 3.0 35.4 + - + +
241J VAL* 3.5 23.8 - - + -
242J LEU 3.3 9.2 - - - +
243J PRO* 4.2 0.4 - - - -
244J VAL* 3.7 3.6 - - - +
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Residues in contact with ILE 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J GLU* 4.6 3.6 - - - +
38J VAL* 4.5 13.2 - - + +
104J HIS* 1.3 79.1 - - - +
106J GLU* 1.3 60.5 + - - +
107J LEU* 3.3 11.9 + - + -
241J VAL* 3.5 3.1 - - - -
242J LEU* 2.7 48.3 + - + +
244J VAL* 3.4 29.6 - - + -
269J TYR* 4.1 12.8 - - + -
272J VAL* 4.5 11.4 - - + -
273J ILE* 3.8 34.1 - - + -
276J ASN* 3.7 23.8 - - + +
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Residues in contact with GLU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ARG* 3.2 37.6 + - - -
37J GLU* 3.4 34.3 + - - +
104J HIS* 3.0 26.3 + - - +
105J ILE* 1.3 71.1 - - - +
107J LEU* 1.3 67.3 + - - +
108J ALA 3.4 1.6 + - - -
240J THR* 4.7 2.9 - - - +
241J VAL* 3.5 11.9 - - - +
276J ASN* 2.9 15.3 + - - -
280J LYS* 4.0 13.0 + - - +
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Residues in contact with LEU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J ILE* 3.3 16.2 + - + +
106J GLU* 1.3 72.9 - - - +
108J ALA* 1.3 63.3 + - - +
109J SER 3.3 15.8 + - - +
110J PRO* 4.8 0.3 - - - +
111J THR* 3.5 25.4 - - - +
239J LEU* 3.9 17.9 - - + +
240J THR* 3.3 26.7 + - - +
242J LEU* 4.2 23.6 - - + -
272J VAL* 4.5 8.7 - - + -
276J ASN* 3.5 19.7 - - - +
299J LEU* 4.4 14.6 - - + -
303J VAL* 4.4 10.1 - - + -
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J GLU 3.4 2.2 + - - -
107J LEU* 1.3 71.6 - - - +
109J SER* 1.3 58.4 + - - +
110J PRO* 4.6 2.0 - - - +
183J GLU* 5.8 0.2 - - - +
276J ASN* 3.3 19.9 + - - +
279J LEU* 3.7 20.4 - - + -
280J LYS* 4.0 22.0 - - + +
283J LEU* 4.4 15.8 - - + +
296J LYS* 5.5 0.3 - - - -
299J LEU* 5.3 0.4 - - - +
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Residues in contact with SER 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J LEU* 3.3 20.4 - - - +
108J ALA* 1.3 78.8 - - - +
110J PRO* 1.3 82.0 + - - +
111J THR* 3.5 4.5 + - - -
141J PHE* 5.5 1.4 - - - -
182J ALA* 5.5 1.0 - - - +
183J GLU* 4.8 5.7 + - - +
279J LEU* 4.5 5.1 - - - +
296J LYS* 3.5 46.7 + - - +
299J LEU* 3.9 11.5 - - - +
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Residues in contact with PRO 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J LEU 5.4 0.7 - - - +
108J ALA 4.6 1.8 - - - +
109J SER* 1.3 102.4 + - - +
111J THR* 1.3 62.0 + - - +
182J ALA* 3.3 17.3 - - + +
183J GLU* 4.2 24.2 - - + +
186J GLN* 3.4 26.9 - - - +
238J ILE* 3.9 9.9 - - + -
239J LEU 3.6 9.6 - - - +
240J THR* 4.4 18.6 - - + +
299J LEU* 5.0 1.2 - - - +
300J GLN* 4.3 2.3 - - - +
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Residues in contact with THR 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J LEU* 3.5 20.5 - - - +
109J SER 3.5 3.8 + - - -
110J PRO* 1.3 80.1 + - - +
112J ALA* 1.3 64.1 + - - +
182J ALA* 4.0 0.7 - - - -
238J ILE* 3.6 5.1 - - - +
239J LEU* 2.5 47.1 + - + +
299J LEU* 3.5 12.3 - - - +
300J GLN* 3.3 30.1 + - - +
303J VAL* 3.6 32.3 - - + -
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Residues in contact with ALA 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J THR* 1.3 74.7 - - - +
113J HIS* 1.3 64.6 + - - +
114J ILE* 4.3 0.3 - - - -
117J LEU* 4.9 4.7 - - + +
124J ILE* 4.9 6.1 - - + -
139J LEU* 3.7 35.4 - - + -
182J ALA* 4.0 2.6 - - - +
238J ILE* 3.7 25.1 - - + +
300J GLN* 3.1 16.2 + - - +
304J ASP* 3.0 22.0 - - - +
307J LEU* 5.1 0.2 - - - +
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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