Contacts of the strand formed by residues 111 - 118 (chain A) 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 THR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY 4.4 1.1 - - - +
110A GLN* 1.3 90.7 + - - +
112A PHE* 1.3 67.6 + - - +
127A GLN* 3.8 12.0 + - + +
128A CYS 3.1 13.0 - - - +
129A ALA* 4.0 8.5 - - + -
151A ASN* 3.3 18.3 + - - +
203A ASN* 4.9 0.2 - - - +
290A GLU 3.2 31.0 - - - +
292A THR* 3.7 14.4 - - + +
295A ASP* 2.7 32.4 + - - +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.5 31.2 - - + -
110A GLN 4.5 0.2 - - - -
111A THR* 1.3 79.8 - - - +
113A SER* 1.3 59.2 + - - +
114A VAL* 3.6 22.0 - - + -
127A GLN* 3.1 11.2 - - - +
128A CYS* 2.8 43.8 + - + +
129A ALA 4.4 0.7 - - - -
130A MET* 4.1 18.6 - - + -
136A ILE* 4.0 23.3 - - + -
149A GLY* 3.6 19.7 - - - -
150A PHE 3.5 11.4 - - - +
151A ASN* 3.6 15.7 - - - +
160A CYS* 3.7 9.4 - - - -
161A TYR* 3.9 27.8 - + + -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.4 5.9 - - - -
8A PHE* 2.8 31.6 + - - -
112A PHE* 1.3 72.3 - - - +
114A VAL* 1.3 61.4 + - - +
125A VAL* 4.4 2.9 - - - -
126A TYR 3.5 4.9 - - - -
127A GLN* 2.5 20.1 + - - -
149A GLY* 2.9 5.5 - - - -
150A PHE* 2.8 62.7 + - - -
151A ASN* 4.9 0.4 + - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.6 30.3 - - + -
113A SER* 1.3 73.0 - - - +
115A LEU* 1.3 61.5 + - - +
116A ALA 3.8 8.2 + - - +
124A GLY 3.7 0.7 - - - +
125A VAL* 3.2 10.4 - - - +
126A TYR* 2.8 60.9 + - + +
128A CYS* 4.0 19.3 - - + -
136A ILE* 4.7 7.6 - - + -
140A PHE* 3.7 18.4 - - + -
147A SER* 5.1 1.3 - - - -
148A VAL 3.6 8.7 - - - +
149A GLY* 4.3 3.6 - - - +
150A PHE* 4.4 0.7 - - - -
161A TYR* 5.0 2.7 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.9 24.2 - - - +
13A VAL* 3.7 27.4 - - + -
14A GLU* 3.9 23.1 - - + +
17A MET* 4.0 14.8 - - + -
114A VAL* 1.3 71.5 - - - +
116A ALA* 1.3 65.1 + - - +
117A CYS* 3.4 13.3 + - - -
122A PRO* 3.8 20.4 - - + -
124A GLY 3.4 13.5 - - - +
125A VAL* 4.3 3.6 - - + +
147A SER* 3.5 15.9 - - - -
148A VAL* 3.2 12.7 + - + +
150A PHE* 4.1 15.1 - - + -
9B PRO* 4.3 7.4 - - + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.7 5.8 - - - +
115A LEU* 1.3 71.2 - - - +
117A CYS* 1.3 52.1 + - - +
118A TYR* 4.6 8.3 - - + +
122A PRO* 3.6 1.7 - - - +
123A SER* 2.7 44.3 + - - +
124A GLY* 2.9 17.2 + - - +
126A TYR* 4.1 21.8 - - + +
139A SER 4.4 10.8 - - - +
140A PHE* 5.2 4.0 - - + -
144A SER* 6.0 0.4 - - - -
147A SER* 4.0 6.7 - - - -
6B MET* 4.9 5.2 - - + -
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Residues in contact with CYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.8 34.1 - - + -
28A ASN* 3.1 36.0 + - - +
115A LEU* 3.6 17.5 - - - -
116A ALA* 1.3 70.5 - - - +
118A TYR* 1.3 72.8 + - - +
120A GLY 4.9 0.4 - - - -
121A SER 3.5 10.8 - - - +
122A PRO* 3.5 23.6 - - - -
144A SER* 3.3 13.0 - - - -
147A SER* 3.1 9.8 + - - +
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASN* 3.8 0.9 - - - -
116A ALA* 4.6 5.5 - - + +
117A CYS* 1.3 83.5 - - - +
119A ASN* 1.3 81.2 + - - +
120A GLY 3.2 0.7 - - - -
121A SER* 3.0 24.6 + - - +
123A SER* 3.6 24.5 - - - -
139A SER 4.4 3.6 + - - -
140A PHE* 4.0 4.7 - - - -
141A LEU* 3.1 35.9 + - + +
142A ASN 3.4 26.5 - - - -
143A GLY* 3.7 9.6 - - - -
144A SER* 3.6 21.6 - - - -
302B GLY* 3.3 37.0 - - - +
303B VAL 5.9 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