Contacts of the strand formed by residues 65 - 76 (chain B) in PDB entry 1YTB
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 PRO 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ILE 4.2 4.3 - - - +
64B VAL* 1.3 89.5 - - - +
66B THR* 1.3 61.7 + - - +
67B LEU* 3.9 2.1 + - - +
163B SER 3.6 13.5 - - - +
164B CYS* 4.1 8.9 - - + -
214B LEU* 4.4 8.7 - - + -
223B ILE* 3.8 27.8 - - + -
224B TYR* 3.6 36.7 + - + -
227B PHE* 3.8 34.1 - - + -
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Residues in contact with THR 66 (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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64B VAL 3.6 4.4 + - - -
65B PRO* 1.3 71.5 - - - +
67B LEU* 1.3 70.9 + - - +
68B GLN* 3.5 25.0 + - - +
127B LYS* 6.1 1.3 - - + -
162B GLY* 3.2 2.3 - - - -
163B SER 2.9 34.5 + - - -
164B CYS* 5.8 0.5 - - - +
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Residues in contact with LEU 67 (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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65B PRO 3.9 1.3 + - - +
66B THR* 1.3 84.1 - - - +
68B GLN* 1.3 60.4 + - - +
69B ASN 3.9 0.2 - - - -
70B ILE* 4.3 15.7 - - + -
127B LYS* 3.5 40.6 - - - +
128B SER* 5.0 4.7 - - - -
129B GLU 5.8 1.1 - - - +
160B ILE* 4.1 18.8 - - + -
161B VAL 3.6 6.3 - - - +
162B GLY* 4.7 0.2 - - - -
220B ARG* 4.2 25.6 - - + +
223B ILE* 4.3 23.6 - - + -
224B TYR* 4.3 23.3 - - + +
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Residues in contact with GLN 68 (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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66B THR* 3.6 29.6 - - - +
67B LEU* 1.3 76.6 - - - +
69B ASN* 1.3 61.4 + - + +
125B GLY 4.7 0.5 - - - +
126B ALA 4.1 0.2 - - - +
127B LYS* 2.8 50.7 + - - +
161B VAL* 2.8 19.1 + - + +
162B GLY 4.4 1.1 - - - -
163B SER* 3.0 32.7 + - - +
25D T 3.4 13.8 - - + +
26D A 3.6 34.0 - - - +
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Residues in contact with ASN 69 (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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67B LEU 3.9 0.4 - - - -
68B GLN* 1.3 81.1 - - - +
70B ILE* 1.3 66.7 + - - +
71B VAL* 3.9 6.3 - - - +
124B THR* 3.4 3.3 + - - -
125B GLY* 3.0 31.9 + - - -
126B ALA 3.2 7.7 + - - -
159B ASN 4.2 0.4 - - - +
160B ILE* 3.5 2.8 - - - -
161B VAL* 2.9 37.5 + - + +
24D A 3.1 33.7 + - - -
25D T 3.2 39.6 + - - +
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Residues in contact with ILE 70 (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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67B LEU* 4.3 11.2 - - + -
69B ASN* 1.3 81.0 + - - +
71B VAL* 1.3 63.8 + - - +
123B VAL 3.7 1.7 - - - +
124B THR* 3.7 4.2 - - - -
125B GLY 3.7 17.0 + - - -
126B ALA* 2.8 16.9 + - + +
127B LYS* 3.4 35.7 - - - +
128B SER* 3.5 11.0 - - - +
129B GLU* 4.5 2.5 - - + +
132B SER* 3.8 29.1 + - - +
157B ILE* 4.0 27.4 - - + -
159B ASN 3.5 3.4 - - - -
160B ILE* 4.1 26.7 - - + -
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Residues in contact with VAL 71 (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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69B ASN* 3.9 7.4 - - - +
70B ILE* 1.3 74.8 - - - +
72B ALA* 1.3 63.7 + - - +
122B VAL* 4.0 13.9 - - + -
123B VAL 3.5 4.5 - - - +
124B THR* 3.5 20.6 - - - +
157B ILE* 3.6 2.8 - - - +
158B GLN* 2.8 31.8 + - + -
159B ASN* 2.8 28.1 + - + +
161B VAL* 6.0 0.2 - - + -
6D T 3.4 22.9 - - - +
7D A 3.9 27.8 - - + +
24D A 3.7 10.8 - - + +
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Residues in contact with ALA 72 (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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70B ILE 4.2 0.2 - - - -
71B VAL* 1.3 75.9 - - - +
73B THR* 1.3 63.9 + - - +
74B VAL* 5.3 0.4 - - + -
122B VAL* 3.3 7.8 - - - +
123B VAL* 2.9 38.0 + - + +
132B SER* 3.5 23.8 - - - +
155B PHE* 3.5 22.2 - - + -
156B LYS 3.2 15.5 - - - +
157B ILE* 4.1 3.4 - - + -
158B GLN* 4.3 2.2 - - - +
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Residues in contact with THR 73 (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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72B ALA* 1.3 76.6 - - - +
74B VAL* 1.3 65.5 + - - +
121B MET 3.4 4.5 - - - +
122B VAL* 4.0 11.0 - - + -
154B ASP 3.3 4.6 + - - +
155B PHE* 3.3 6.2 - - - -
156B LYS* 2.9 34.8 + - - +
158B GLN* 2.9 23.5 + - + +
7D A 3.9 45.3 - - + +
8D A 4.5 8.5 - - - -
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Residues in contact with VAL 74 (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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72B ALA 5.3 0.7 - - - -
73B THR* 1.3 82.3 - - - +
75B THR* 1.3 73.4 + - - +
76B LEU* 4.0 8.5 - - + -
120B LYS* 3.7 3.5 - - - +
121B MET* 2.9 54.6 + - + +
123B VAL* 4.7 3.8 - - + -
136B SER* 3.6 30.3 - - - +
152B PHE* 4.0 18.2 - - + -
153B THR 3.3 17.7 - - - +
154B ASP 4.2 1.6 - - - -
155B PHE* 3.9 13.9 - - + -
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Residues in contact with THR 75 (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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156A LYS* 6.3 0.9 - - - +
74B VAL* 1.3 74.7 - - - +
76B LEU* 1.3 61.4 + - - +
77B GLY* 3.7 16.2 - - - +
119B GLY 4.2 2.7 - - - +
120B LYS* 3.8 33.3 - - + +
151B LYS 3.2 6.6 - - - +
153B THR* 2.8 34.1 + - - +
154B ASP* 3.3 31.2 + - - +
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Residues in contact with LEU 76 (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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74B VAL* 4.1 6.5 - - + -
75B THR* 1.3 71.7 - - - +
77B GLY* 1.3 61.8 + - - +
78B CYS* 3.5 3.4 - - - +
80B LEU* 4.2 21.1 - - + -
115B ILE* 4.6 3.6 - - + -
119B GLY* 2.8 27.6 + - - +
121B MET* 4.0 38.4 - - + -
140B ALA* 3.9 26.0 - - + -
143B ILE* 4.3 18.2 - - + -
149B ALA 3.9 1.2 - - - +
150B ALA* 3.4 18.2 - - + -
151B LYS* 3.0 39.3 + - - +
153B THR* 5.1 0.7 - - - -
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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