Contacts of the strand formed by residues 86 - 93 (chain A) in PDB entry 2YGN
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLN* 4.1 6.2 + - - +
84A ILE* 3.2 16.5 - - - +
85A HIS* 1.3 79.9 + - - +
87A MET* 1.3 61.5 + - - +
88A ASN* 5.2 3.7 + - - -
135A GLN* 5.0 12.4 + - - -
136A VAL 3.2 16.6 - - - -
137A GLY* 3.9 7.6 - - - -
138A PHE* 3.9 6.7 - - - -
1180A NAG 5.8 1.9 - - - +
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Residues in contact with MET 87 (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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40A ILE* 3.6 34.3 - - + -
44A GLN* 3.4 18.2 - - + +
48A LEU* 3.6 29.2 - - + -
80A ILE* 5.2 1.8 - - - -
84A ILE* 5.1 3.6 - - + -
86A SER* 1.3 75.1 - - - +
88A ASN* 1.3 66.6 + - - +
89A PHE* 3.7 22.2 + - + -
134A VAL 3.6 0.9 - - - +
135A GLN* 3.5 2.1 - - - -
136A VAL* 2.8 39.9 + - + +
138A PHE* 3.8 18.4 - - + -
1179A PCF 3.7 33.9 - - + -
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Residues in contact with ASN 88 (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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40A ILE* 3.9 13.7 - - - +
41A ASP* 4.1 17.4 + - - +
44A GLN* 2.7 29.5 + - + +
86A SER* 5.2 3.1 + - - -
87A MET* 1.3 74.2 + - - +
89A PHE* 1.3 62.6 + - - +
133A VAL* 3.7 15.1 - - + +
134A VAL 3.7 2.9 - - - -
135A GLN* 3.3 21.8 - - - +
1180A NAG 1.4 63.7 + - - +
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Residues in contact with PHE 89 (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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38A LEU* 4.0 9.6 - - + -
39A TRP 3.7 2.9 - - - -
40A ILE* 3.8 15.9 - - + -
57A ILE* 3.7 27.4 - - + -
87A MET* 3.7 39.7 - - + -
88A ASN* 1.3 76.8 - - - +
90A THR* 1.3 62.2 + - - +
91A TRP 4.2 0.2 + - - -
133A VAL* 3.2 4.9 - - - -
134A VAL* 2.8 37.3 + - + +
136A VAL* 3.8 30.1 - - + -
1179A PCF 3.8 66.4 - - + -
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Residues in contact with THR 90 (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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38A LEU* 3.3 5.1 - - - +
39A TRP* 2.7 80.1 + - + +
41A ASP* 4.2 19.1 + - - +
89A PHE* 1.3 75.9 + - - +
91A TRP* 1.3 64.5 + - - +
131A ALA* 4.2 5.4 - - + -
132A SER 3.4 21.5 - - - +
133A VAL* 3.7 15.6 - - + +
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Residues in contact with TRP 91 (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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37A TYR 3.2 12.3 - - - +
38A LEU* 4.0 8.7 - - + -
39A TRP* 4.5 2.5 - - - -
90A THR* 1.3 75.2 - - - +
92A GLN* 1.3 64.2 + - - +
101A TYR* 3.3 62.4 - + + -
103A PHE* 4.2 11.0 - + - -
121A VAL* 4.6 2.9 - - + +
127A VAL* 4.2 12.8 - - + -
128A PRO* 3.4 27.3 - - + +
130A MLY 4.2 1.2 - - - +
131A ALA* 3.4 1.4 - - - -
132A SER* 3.0 43.4 + - - -
134A VAL* 3.3 31.6 - - + +
154A VAL* 5.0 4.0 - - + -
156A VAL* 5.4 0.2 - - + -
1179A PCF 4.1 43.3 - - + -
1181A ACT 4.7 4.7 + - - -
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Residues in contact with GLN 92 (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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35A SER 3.6 0.7 - - - +
36A LEU* 3.5 3.5 - - - +
37A TYR* 2.9 45.9 + - + +
39A TRP* 3.9 20.1 - - + -
91A TRP* 1.3 78.5 - - - +
93A ALA* 1.3 57.2 + - - +
94A ALA* 3.5 24.4 - - - +
127A VAL* 3.8 8.3 - - - +
128A PRO 3.3 9.2 - - - +
129A HIS 3.0 19.0 + - - -
131A ALA* 3.6 29.4 - - - +
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Residues in contact with ALA 93 (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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35A SER* 4.0 6.3 - - - -
36A LEU* 4.3 4.0 - - + +
92A GLN* 1.3 70.3 - - - +
94A ALA* 1.3 59.0 + - - +
95A GLY 3.2 5.1 + - - -
97A ALA 4.5 1.1 - - - +
99A TYR* 3.9 26.9 - - + +
127A VAL* 3.7 29.4 - - + +
128A PRO 2.8 8.6 + - - +
129A HIS* 2.6 44.3 + - + +
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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