Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 2YDW
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASN* 1.3 87.2 + - - +
78A GLN* 3.2 18.6 - - + +
79A LEU* 3.4 30.3 + - - +
80A GLN* 3.1 22.0 + - - +
136A TRP 4.5 9.4 + - - -
137A ALA* 5.7 0.4 - - - -
138A ALA 6.0 2.0 - - - +
182A GLN* 5.4 4.3 - - + +
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Residues in contact with ASN 77 (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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76A THR* 1.3 86.2 - - - +
78A GLN* 1.3 69.1 + - - +
80A GLN* 3.4 8.2 + - - +
81A TYR* 3.1 23.0 + - - +
181A PRO* 3.8 13.7 - - + +
182A GLN* 3.5 29.6 + - - +
97B TRP* 4.7 3.5 - - - -
161B ASP* 3.4 24.5 + - - +
1182B WSH 3.9 27.8 - - + -
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Residues in contact with GLN 78 (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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76A THR* 3.2 8.9 - - + +
77A ASN* 1.3 92.5 + - - +
79A LEU* 1.3 57.4 + - - +
81A TYR* 3.3 4.1 + - - +
82A LEU* 3.0 32.9 + - - +
138A ALA* 3.3 31.7 + - + +
180A MET* 3.9 17.3 - - + +
181A PRO* 2.8 29.6 + - - +
182A GLN* 3.4 30.0 + - + +
178C ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 79 (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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76A THR* 3.4 30.9 + - - +
77A ASN 3.4 0.2 - - - -
78A GLN* 1.3 74.4 - - - +
80A GLN* 1.3 60.7 + - - +
82A LEU* 3.4 4.9 + - + +
83A HIS* 3.0 29.1 + - - +
130A LEU* 3.8 15.9 - - + +
133A ASN* 6.5 0.4 - - - -
135A TYR* 3.4 48.7 - - + +
136A TRP 4.5 7.9 - - - +
137A ALA 3.9 1.1 - - - +
138A ALA* 3.8 25.8 - - - +
141A CYS* 4.1 14.1 - - + -
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Residues in contact with GLN 80 (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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76A THR 3.1 13.8 + - - +
77A ASN* 3.6 11.0 - - - +
78A GLN 3.3 0.2 - - - -
79A LEU* 1.3 77.4 - - - +
81A TYR* 1.3 52.2 + - - +
83A HIS* 3.3 7.8 + - - +
84A LYS* 2.8 80.5 + - - +
97B TRP* 3.7 19.7 - - + -
108B LEU* 3.7 24.8 - - - +
1182B WSH 3.8 15.3 - - + -
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Residues in contact with TYR 81 (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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77A ASN 3.1 13.6 + - - +
78A GLN 3.5 7.9 - - - +
79A LEU 3.3 0.2 - - - -
80A GLN* 1.3 73.8 - - - +
82A LEU* 1.3 62.0 + - - +
85A VAL* 2.7 70.7 + - + +
86A VAL* 3.3 19.1 + - + -
176A LYS* 2.7 35.0 + - - +
177A VAL* 4.8 0.2 - - - -
179A SER* 3.6 26.3 - - - -
180A MET* 3.6 21.3 - - + -
181A PRO* 3.8 18.8 - - + -
94B GLN* 5.5 6.0 - - + +
97B TRP* 3.8 29.3 - + + -
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Residues in contact with LEU 82 (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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78A GLN 3.0 19.8 + - - +
79A LEU* 3.7 8.5 - - + +
81A TYR* 1.3 76.4 - - + +
83A HIS* 1.3 54.5 + - - +
86A VAL* 3.3 29.7 + - + +
87A MET* 2.6 35.5 + - - +
130A LEU* 4.4 3.7 - - + +
138A ALA* 3.6 36.6 - - + +
141A CYS* 3.7 30.5 - - + -
142A MET* 4.2 8.3 - - + -
145A PHE* 5.2 1.6 - - + -
173A PHE* 4.9 2.7 - - + -
177A VAL* 4.1 14.8 - - + -
180A MET* 4.0 15.7 - - - -
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Residues in contact with HIS 83 (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 LEU 3.0 17.9 + - - +
80A GLN* 3.6 9.4 + - - +
82A LEU* 1.3 76.9 - - - +
84A LYS* 1.3 81.9 + - + +
87A MET* 3.5 9.9 - - + +
88A LYS* 3.4 21.5 + - - +
127A LYS* 4.9 6.2 + - + +
130A LEU* 4.0 34.2 + - + +
131A GLU* 3.9 38.2 + - + +
107B LYS* 6.2 4.7 - - + -
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Residues in contact with LYS 84 (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 GLN* 2.8 56.7 + - - +
83A HIS* 1.3 95.2 - - + +
85A VAL* 1.3 59.2 - - - +
88A LYS* 3.2 43.6 + - - +
97B TRP* 3.6 30.0 - - + +
100B ARG* 5.7 1.9 + - - -
101B GLN* 4.7 17.1 - - - +
107B LYS* 5.9 8.7 - - - +
108B LEU* 4.8 4.4 - - - +
1182B WSH 4.5 10.1 - - - -
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Residues in contact with VAL 85 (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* 2.7 46.7 + - + +
84A LYS* 1.3 75.8 - - - +
86A VAL* 1.3 66.3 + - - +
87A MET 3.7 0.2 - - - -
88A LYS* 4.2 1.4 - - - +
89A ALA* 3.4 22.5 + - - +
176A LYS* 3.7 30.7 + - + +
97B TRP* 3.5 44.6 - - + -
100B ARG* 5.8 1.1 - - - +
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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