Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 2YNU
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 GLN 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASN 2.7 14.3 + - - +
79A GLN* 3.4 10.6 + - + +
80A ALA 2.7 24.2 + - - -
100A THR* 5.8 0.7 - - - -
105A GLY 4.0 1.0 + - - +
106A TYR* 1.3 70.8 - - - +
109A VAL* 1.3 67.6 + - - +
110A MET* 3.2 33.1 + - - +
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Residues in contact with VAL 109 (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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80A ALA* 3.3 14.4 - - + +
82A ILE* 3.7 29.4 - - + -
95A LEU 5.7 0.2 - - - +
96A LEU* 3.7 22.0 - - + -
99A ALA* 4.0 26.2 - - + -
100A THR* 5.0 6.2 - - + +
106A TYR 3.7 2.0 + - - +
107A GLN* 1.3 76.4 + - - +
110A MET* 1.3 62.7 + - - +
111A ALA 3.9 11.7 - - - +
134A ILE* 3.7 38.7 - - + +
135A PRO* 5.1 0.5 - - - +
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Residues in contact with MET 110 (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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79A GLN* 3.5 46.9 - - + +
80A ALA 2.8 14.3 + - - +
81A TYR* 3.8 29.4 - - + +
107A GLN* 3.5 40.2 - - - +
109A VAL* 1.3 73.9 - - - +
111A ALA* 1.3 60.2 + - + +
134A ILE* 4.2 0.2 - - - -
135A PRO* 3.1 27.5 - - - +
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Residues in contact with ALA 111 (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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80A ALA 4.0 0.6 + - - -
81A TYR* 3.6 23.8 - - + -
82A ILE 3.0 21.7 + - - -
109A VAL* 3.5 8.2 - - - +
110A MET* 1.3 81.5 - - - +
112A SER* 1.3 61.0 - - - +
134A ILE* 4.0 7.5 - - - +
135A PRO 3.1 13.5 - - - +
137A TYR* 3.9 24.5 - - + -
182A LEU* 4.7 6.7 - - + -
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Residues in contact with SER 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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82A ILE* 3.1 23.8 - - - -
85A THR* 4.5 8.8 - - - +
111A ALA* 1.3 76.9 - - - +
113A ILE* 1.4 57.8 + - - +
114A SER* 5.2 1.4 + - - -
125A ILE* 5.2 1.6 - - - +
128A LEU* 3.4 21.4 - - - +
134A ILE* 4.7 0.4 - - - +
135A PRO 3.0 4.8 + - - -
136A THR* 3.4 25.5 - - - +
137A TYR* 2.8 36.5 + - - +
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Residues in contact with ILE 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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81A TYR* 6.4 0.4 - - + -
82A ILE 2.9 11.6 + - - +
83A ILE* 3.7 21.6 - - + +
84A ASP* 2.9 26.2 + - - +
112A SER* 1.4 75.0 - - - +
114A SER* 1.3 64.9 + - - +
115A THR* 4.8 2.1 - - + +
137A TYR* 3.2 31.4 - - + +
138A THR* 3.9 3.4 - - - -
172A PHE* 3.9 10.1 - - + -
182A LEU* 3.9 22.4 - - + -
187A ILE* 5.1 2.7 - - + -
189A LEU* 3.3 41.3 - - + -
201A ILE* 3.9 15.0 - - + -
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Residues in contact with SER 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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84A ASP* 3.3 5.2 - - - -
85A THR* 4.3 5.4 + - - +
112A SER* 5.2 1.4 + - - -
113A ILE* 1.3 86.0 - - - +
115A THR* 1.3 63.5 + - - +
116A HIS 3.4 2.8 + - - +
121A ARG 2.6 25.9 + - - -
122A THR* 3.6 22.4 - - - +
125A ILE* 3.9 12.5 - - - +
137A TYR 3.1 6.5 + - - -
138A THR* 3.9 24.6 - - - +
139A SER 4.8 0.7 + - - -
142A THR* 4.7 1.7 + - - +
201A ILE* 4.0 4.0 - - - +
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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