Contacts of the strand formed by residues 121 - 129 (chain B) in PDB entry 6Y2G
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 SER 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B CYS* 4.1 1.6 - - - -
118B TYR* 2.9 34.0 + - - +
119B ASN* 3.2 4.1 + - - -
120B GLY* 1.4 77.4 + - - +
122B PRO* 1.3 72.1 - - - +
123B SER* 3.4 2.8 + - - -
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Residues in contact with PRO 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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9A PRO* 3.7 26.0 - - + +
14B GLU* 4.0 31.9 - - + +
17B MET* 4.4 4.0 - - + -
115B LEU* 3.9 21.1 - - + -
116B ALA 3.6 7.0 - - - +
117B CYS* 3.7 9.6 - - - -
120B GLY 3.7 8.3 - - - +
121B SER* 1.3 88.1 - - - +
123B SER* 1.3 60.1 + - - +
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Residues in contact with SER 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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6A MET* 4.6 10.0 - - - +
8A PHE* 4.5 5.0 - - - -
9A PRO* 3.7 10.6 - - - +
298A ARG* 3.5 18.9 + - - -
116B ALA* 2.8 20.7 + - - +
118B TYR* 3.8 30.0 - - - -
121B SER 3.4 2.9 + - - -
122B PRO* 1.3 73.5 - - - +
124B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 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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6A MET* 3.9 15.9 - - - -
7A ALA 3.2 13.5 - - - -
9A PRO* 3.8 6.5 - - - +
114B VAL 3.8 0.2 - - - +
115B LEU* 3.5 7.5 - - - +
116B ALA* 3.0 29.0 + - - -
123B SER* 1.3 84.2 + - - +
125B VAL* 1.3 63.0 + - - +
126B TYR* 4.9 0.4 - - - -
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Residues in contact with VAL 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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5A LYS 4.5 0.3 - - - +
6A MET* 3.6 2.2 - - - +
7A ALA* 2.9 37.0 + - + +
8A PHE 3.6 24.5 - - - +
9A PRO* 4.4 5.6 - - + -
10A SER 5.1 0.2 - - - +
125A VAL* 4.0 19.1 - - + -
7B ALA* 3.6 20.1 - - + +
8B PHE 4.3 7.9 - - - +
10B SER* 4.4 12.1 - - - +
113B SER* 4.4 6.5 - - - -
114B VAL 3.3 18.2 - - - +
115B LEU* 4.2 8.5 - - + -
124B GLY* 1.3 75.1 - - - +
126B TYR* 1.3 68.6 + - - +
150B PHE* 4.9 1.6 - - + -
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Residues in contact with TYR 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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4A ARG* 3.6 31.2 - - + +
5A LYS 3.9 17.7 - - - +
6A MET* 4.1 22.2 - - + -
7B ALA* 4.2 10.1 - - - -
113B SER* 3.5 0.9 - - - -
114B VAL* 2.8 48.6 + - + -
116B ALA* 4.2 13.7 - - + -
125B VAL* 1.3 83.3 - - - +
127B GLN* 1.3 57.6 + - - +
128B CYS* 3.7 21.8 - - - -
138B GLY* 3.9 10.5 - - - -
139B SER* 3.0 40.8 + - - -
140B PHE* 3.3 19.6 - - - -
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Residues in contact with GLN 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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4A ARG* 2.6 34.0 + - - +
5B LYS* 3.9 25.1 - - + +
6B MET 3.3 29.4 + - - +
7B ALA* 3.5 1.3 - - - +
8B PHE* 4.3 7.2 + - - -
111B THR* 3.5 30.4 + - + -
112B PHE* 3.4 13.8 - - - +
113B SER* 2.7 28.4 + - - -
126B TYR* 1.3 72.9 - - - +
128B CYS* 1.3 62.5 + - - +
290B GLU* 4.4 7.0 - - - +
291B PHE* 6.5 0.4 - - + -
295B ASP* 4.3 6.4 + - - +
298B ARG* 4.2 11.9 - - - +
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Residues in contact with CYS 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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4A ARG* 3.5 21.1 - - - -
111B THR* 3.2 7.6 - - - -
112B PHE* 2.8 47.6 + - + +
114B VAL* 3.9 11.7 - - + -
126B TYR* 3.7 22.9 + - - -
127B GLN* 1.3 74.2 - - - +
129B ALA* 1.3 66.3 + - - +
136B ILE* 4.2 19.1 - - + -
137B LYS 3.8 11.9 - - - +
290B GLU* 3.8 7.9 - - - +
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Residues in contact with ALA 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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109B GLY 4.9 1.8 - - - +
110B GLN 3.5 6.7 - - - +
111B THR* 3.8 18.4 - - + -
112B PHE* 4.6 0.2 - - - -
128B CYS* 1.3 75.8 - - - +
130B MET* 1.3 65.9 + - - +
131B ARG* 3.3 12.9 + - - +
136B ILE* 3.6 19.2 - - - +
137B LYS 4.8 0.5 + - - -
200B ILE* 4.5 13.5 - - + -
290B GLU* 3.1 34.9 + - + +
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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