Contacts of the strand formed by residues 116 - 125 (chain G) in PDB entry 6D6Q
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 HIS 116 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G GLY 5.6 2.0 - - - -
115G ASP* 1.3 73.4 - - - +
117G VAL* 1.3 60.8 + - - +
164G TYR* 3.2 37.9 - + + +
165G GLY 3.3 4.1 + - - -
166G GLN* 3.2 16.9 + - - +
188G ASN* 5.1 2.9 - - - -
190G MET* 3.2 36.1 - - + +
231G PHE 4.6 1.6 - - - +
232G GLY* 4.0 2.1 - - - -
233G MET* 3.2 32.7 + - + +
65L LEU* 6.2 2.7 - - + -
72L TYR* 4.6 22.2 - + - -
73L GLY* 5.8 2.0 - - - -
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Residues in contact with VAL 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 3.8 17.9 - - + +
115G ASP* 3.4 15.9 - - + +
116G HIS* 1.3 80.8 - - - +
118G ILE* 1.3 79.2 + - - +
133G VAL* 3.6 21.1 - - + -
163G ILE 3.7 0.2 - - - +
164G TYR* 3.4 4.9 - - - -
165G GLY* 2.9 34.2 + - - +
167G PHE* 3.6 22.7 - - + -
178G MET* 4.5 6.5 - - + +
232G GLY* 4.6 3.4 - - - -
233G MET* 4.7 4.0 - - + +
234G ASN* 3.2 17.0 - - - +
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Residues in contact with ILE 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G VAL* 1.3 84.0 - - - +
119G GLY* 1.3 69.2 + - - +
120G ILE* 5.4 0.2 - - + -
132G ASP 4.2 2.1 - - - +
133G VAL* 4.4 0.2 - - - -
162G LEU* 4.6 6.3 - - + -
163G ILE 3.1 10.8 - - - +
164G TYR* 4.1 6.1 - - + -
178G MET* 5.7 0.4 - - - -
193G ILE* 5.1 3.1 - - + -
199G LEU* 4.0 13.5 - - + -
230G VAL* 3.8 36.3 - - + +
232G GLY* 4.2 5.9 - - - +
234G ASN* 3.0 26.5 + - - +
236G ARG* 3.4 52.6 + - + +
237G ILE 4.3 0.7 - - - -
238G TRP* 4.2 15.9 - - + -
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Residues in contact with GLY 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G VAL* 4.0 0.4 + - - -
118G ILE* 1.3 77.3 - - - +
120G ILE* 1.3 63.5 + - - +
121G VAL 4.2 0.2 - - - -
131G VAL* 3.4 13.0 - - - -
132G ASP 3.2 14.6 - - - -
133G VAL* 5.3 1.3 - - - -
162G LEU* 3.1 10.4 - - - +
163G ILE* 2.9 32.6 + - - -
178G MET* 5.5 4.0 - - - -
236G ARG* 4.2 1.8 - - - -
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Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR* 4.9 5.4 - - - +
5A PRO* 4.0 31.4 - - + +
6A LEU 5.1 0.4 - - - +
7A SER* 4.3 27.6 - - - +
119G GLY* 1.3 78.8 - - - +
121G VAL* 1.3 74.1 + - - +
122G THR* 3.1 4.7 + - - -
131G VAL* 3.0 6.2 - - - +
132G ASP* 2.9 31.3 + - + +
160G GLY* 4.4 16.8 - - - +
161G ASP 3.7 2.9 - - - -
162G LEU* 4.6 5.2 - - + -
199G LEU* 5.0 11.7 - - + -
236G ARG* 3.8 29.2 - - - +
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Residues in contact with VAL 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 5.5 0.7 - - - +
120G ILE* 1.3 73.0 - - - +
122G THR* 1.3 62.5 + - - +
123G ALA 3.8 16.4 - - - +
124G LYS* 5.9 0.2 - - + -
129G PHE* 3.7 24.0 - - + -
130G LYS 3.7 3.8 - - - +
131G VAL* 3.6 4.0 - - + +
157G VAL* 3.7 22.4 - - + -
158G GLN 4.3 7.2 - - - +
159G VAL* 4.1 13.4 - - + +
160G GLY* 3.2 21.7 + - - -
161G ASP 2.9 20.2 + - - +
163G ILE* 3.2 33.4 - - + -
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Residues in contact with THR 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.3 17.1 - - + +
120G ILE 3.1 11.8 + - - -
121G VAL* 1.3 73.5 - - - +
123G ALA* 1.3 63.0 + - + +
130G LYS* 2.6 20.9 + - + -
131G VAL 4.0 0.6 - - - -
132G ASP* 3.5 20.7 + - - +
138G PRO* 5.2 6.7 - - + +
159G VAL* 4.0 12.2 - - - +
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Residues in contact with ALA 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G VAL* 3.6 6.2 - - - +
122G THR* 1.3 83.4 - - + +
124G LYS* 1.3 64.3 + - - +
129G PHE* 3.1 7.2 - - - +
130G LYS* 2.8 34.2 + - + +
159G VAL* 4.5 13.0 - - - -
29O C 6.3 0.9 - - - +
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Residues in contact with LYS 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G VAL* 5.9 0.4 - - + -
123G ALA* 1.3 80.0 - - - +
125G SER* 1.3 60.3 + - - +
126G GLY 4.1 9.6 + - - +
128G ILE 4.5 1.3 - - - +
129G PHE* 3.5 21.8 - - + +
130G LYS 4.6 0.2 - - - +
157G VAL 5.5 6.9 + - - +
158G GLN* 5.5 4.6 + - - +
159G VAL* 5.0 10.7 - - + +
29O C 4.2 16.3 + - - -
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Residues in contact with SER 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G LYS* 1.3 70.7 - - - +
126G GLY* 1.3 64.5 + - - +
127G ASP 2.8 4.2 + - - -
128G ILE* 2.7 45.5 + - - +
130G LYS* 4.5 16.0 - - - +
29O C 4.1 27.1 - - - -
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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