Contacts of the strand formed by residues 121 - 129 (chain B) in PDB entry 6C9G
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B PRO 3.3 1.2 + - - -
120B GLU* 1.3 81.5 - - - +
122B GLU* 1.3 64.1 + - - -
123B HIS* 3.8 11.1 - - - -
153B ILE 3.8 0.7 - - - +
154B GLN* 3.6 7.1 - - - +
155B VAL* 3.2 26.9 + - - +
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Residues in contact with GLU 122 (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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96B SER* 4.7 1.2 + - - -
121B GLY* 1.3 72.5 - - - -
123B HIS* 1.3 75.4 + - - +
124B GLN* 3.6 22.7 + - + -
152B ILE* 3.5 21.2 - - + +
154B GLN* 3.4 30.4 + - - +
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Residues in contact with HIS 123 (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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96B SER* 3.4 16.9 + - - +
97B PHE* 4.0 31.6 - + + +
118B LEU* 3.9 17.7 - - + +
119B PRO* 3.2 46.8 + - + +
121B GLY* 3.8 9.0 - - - -
122B GLU* 1.3 84.7 + - - +
124B GLN* 1.3 64.3 + - - +
151B ASN 4.1 0.2 - - - +
152B ILE* 3.4 2.6 - - - +
153B ILE* 2.8 55.3 + - + +
155B VAL* 4.2 3.8 - - + -
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Residues in contact with GLN 124 (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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95B GLY* 3.1 2.4 - - - -
96B SER* 2.9 35.9 + - - +
97B PHE* 4.2 1.8 - - - -
100B TRP* 3.7 9.7 - - + -
122B GLU* 3.6 20.1 + - + +
123B HIS* 1.3 76.8 - - - +
125B TYR* 1.3 62.4 + - - +
142B VAL* 3.4 36.2 - - + +
150B ASN* 3.3 25.2 + - - +
151B ASN 3.3 6.7 - - - +
152B ILE* 4.1 8.5 - - + +
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Residues in contact with TYR 125 (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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82B PHE* 3.8 29.8 - + - -
93B LEU* 3.6 17.5 - - + -
94B SER 3.1 13.9 - - - +
95B GLY* 3.8 0.7 - - - -
97B PHE* 3.8 17.7 - + + -
100B TRP* 4.1 5.1 - - - -
123B HIS 4.3 0.4 - - - -
124B GLN* 1.3 77.5 - - - +
126B LYS* 1.3 63.2 + - - +
127B PHE* 3.6 25.6 - + - -
139B GLU* 3.9 24.4 + - - +
150B ASN* 3.6 2.9 - - - +
151B ASN* 2.8 66.2 + - + +
152B ILE 4.2 2.5 + - - -
153B ILE* 4.0 31.1 - - + +
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Residues in contact with LYS 126 (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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93B LEU* 3.8 4.3 - - - +
94B SER* 2.7 34.2 + - - +
100B TRP* 4.5 7.9 - - + -
125B TYR* 1.3 78.6 - - - +
127B PHE* 1.3 75.8 - - - +
133B TRP* 4.0 32.2 - - + +
134B THR* 3.3 19.7 - - - +
135B HIS* 5.0 4.0 - - - +
148B THR* 3.8 15.6 - - - +
149B VAL 3.1 30.6 + - - +
150B ASN* 3.5 16.5 + - - +
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Residues in contact with PHE 127 (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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82B PHE* 4.9 7.9 - + + -
83B ARG 4.6 11.7 - - - -
84B TRP* 3.6 41.5 - + + -
91B VAL* 4.2 10.3 - - + -
92B TYR 3.4 14.8 - - - +
93B LEU* 3.9 16.6 - - + -
105B LEU* 3.9 18.4 - - + -
125B TYR* 3.6 31.2 - + - -
126B LYS* 1.3 76.1 - - - +
128B PHE* 1.3 60.4 + - - +
129B VAL* 4.0 16.2 - - + -
133B TRP* 3.4 10.8 - - - -
134B THR 2.8 41.8 + - - +
136B ASP* 4.3 10.8 - - + -
151B ASN* 4.1 7.2 - - - -
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Residues in contact with PHE 128 (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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90B GLU 3.7 1.7 - - - +
91B VAL* 3.4 4.2 - - - -
92B TYR* 2.9 62.4 + + + -
102B LYS* 3.5 28.3 - - - -
127B PHE* 1.3 73.0 - - - +
129B VAL* 1.3 59.7 + - - +
130B ASP 4.0 0.8 + - - -
131B GLY* 3.3 42.4 - - - -
132B GLN 3.5 7.2 - - - -
133B TRP* 3.2 57.4 - + + -
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Residues in contact with VAL 129 (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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84B TRP* 3.7 37.2 - - + +
87B GLY 4.0 17.7 - - - +
90B GLU 3.7 2.5 - - - +
91B VAL* 3.9 22.4 - - + -
127B PHE* 4.1 11.7 - - + -
128B PHE* 1.3 74.6 - - - +
130B ASP* 1.3 78.7 + - + +
131B GLY 3.3 0.7 - - - -
132B GLN* 2.9 27.7 + - + +
134B THR* 3.9 13.0 - - + +
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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