Contacts of the strand formed by residues 65 - 77 (chain B) in PDB entry 1Y7V
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 LEU 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B GLY* 1.3 73.0 - - - +
66B LEU* 1.3 69.1 + - - +
67B LEU* 4.0 20.4 - - + -
439B SER* 3.9 5.4 - - - +
440B GLN* 3.8 33.2 + - + +
442B ASN* 3.8 41.3 - - + +
444B LEU* 4.0 17.0 - - + -
468B VAL* 4.2 9.0 - - + -
469B PRO 3.8 16.2 + - - +
470B LEU* 3.5 17.6 - - + +
471B THR* 3.0 27.0 + - - -
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Residues in contact with LEU 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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60B HIS* 4.7 8.7 - - + +
64B GLY 4.2 4.3 - - - +
65B LEU* 1.3 77.0 - - - +
67B LEU* 1.3 61.9 + - - +
68B THR* 3.8 18.1 + - - +
437B VAL 3.5 1.6 - - - +
438B ALA* 3.3 1.6 - - - -
439B SER* 2.6 56.8 + - - +
471B THR* 3.4 29.6 - - + +
473B LYS* 3.6 30.3 - - + -
479B PHE* 4.1 11.4 - - + -
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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
----------------------------------------------------------
65B LEU* 4.0 18.6 - - + -
66B LEU* 1.3 80.1 - - - +
68B THR* 1.3 57.6 - - - +
69B LEU 3.8 0.2 + - - -
436B LEU* 4.1 20.4 - - + +
437B VAL 3.1 4.7 - - - +
438B ALA* 3.8 23.6 - - + +
442B ASN* 4.6 3.1 - - - +
444B LEU* 5.4 3.4 - - + -
446B ALA* 4.1 25.8 - - + -
458B VAL* 5.3 1.3 - - + -
460B VAL* 4.7 7.4 - - + -
470B LEU* 3.8 29.4 - - + -
471B THR 3.0 9.4 + - - +
472B ILE* 3.3 12.5 - - + +
473B LYS 2.7 30.6 + - - +
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Residues in contact with THR 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 LEU* 3.8 22.7 + - - +
67B LEU* 1.3 73.1 - - - +
69B LEU* 1.3 75.8 + - - +
70B GLN* 3.6 3.9 + - + +
436B LEU* 3.3 4.6 - - - -
437B VAL* 2.7 52.6 + - + +
473B LYS* 3.6 30.2 - - + +
475B PRO* 4.8 4.0 - - + -
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Residues in contact with LEU 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 3.8 1.4 + - - -
68B THR* 1.3 84.8 - - - +
70B GLN* 1.3 60.3 + - - +
71B PRO* 3.3 29.6 - - + +
434B VAL* 3.9 11.0 - - + -
435B GLY 3.7 3.8 - - - +
436B LEU* 3.9 8.0 - - + +
448B ALA* 3.6 30.5 - - + -
449B LEU 5.3 1.8 - - - +
450B MET* 5.5 2.9 - - + -
456B ALA* 4.9 6.5 - - + -
457B VAL 6.2 0.2 - - - +
458B VAL* 4.6 9.0 - - + -
472B ILE* 5.6 1.1 - - + -
473B LYS 2.9 17.5 + - - +
474B ASP* 3.8 30.1 - - + +
475B PRO* 3.6 8.8 - - - +
494B TRP* 4.6 10.5 - - + -
496B ARG* 3.9 12.1 - - - +
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Residues in contact with GLN 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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68B THR* 3.6 11.2 - - + +
69B LEU* 1.3 78.7 - - - +
71B PRO* 1.3 53.6 - - - +
72B GLU* 2.6 18.1 + - + -
73B GLN* 2.6 56.8 + - + +
434B VAL* 4.6 0.2 - - - -
435B GLY 3.0 17.2 + - - +
436B LEU 4.1 5.4 + - - -
437B VAL* 3.3 41.7 - - + +
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Residues in contact with PRO 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 LEU* 3.3 23.4 - - + +
70B GLN* 1.3 85.2 - - - +
72B GLU* 1.3 72.6 + - + +
73B GLN 3.3 0.2 - - - -
74B LYS* 2.8 34.3 + - - +
434B VAL* 3.9 17.1 - - + +
450B MET* 4.3 8.7 - - - -
475B PRO* 4.4 12.1 - - + -
496B ARG* 3.4 35.0 - - - +
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Residues in contact with GLU 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 GLN* 2.6 7.2 + - + -
71B PRO* 1.3 89.5 - - + +
73B GLN* 1.3 58.8 + - - +
74B LYS* 3.3 28.2 + - - +
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Residues in contact with GLN 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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70B GLN* 2.6 46.3 + - + +
72B GLU* 1.3 71.3 - - - +
74B LYS* 1.3 61.4 + - - +
75B PHE* 3.6 19.6 - - + -
434B VAL* 3.1 8.3 - - - +
435B GLY* 3.0 31.1 + - - +
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Residues in contact with LYS 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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71B PRO 2.8 29.4 + - - +
72B GLU* 3.3 28.2 + - - +
73B GLN* 1.3 73.8 - - - +
75B PHE* 1.3 68.1 + - - +
432B GLN* 3.2 34.6 + - - +
433B ARG 3.9 2.5 - - - -
434B VAL* 4.3 6.3 - - + +
450B MET* 3.9 27.3 - - - +
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Residues in contact with PHE 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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73B GLN* 3.6 36.6 - - + -
74B LYS* 1.3 77.7 - - - +
76B GLN* 1.3 76.2 + - - +
77B LYS* 3.8 0.5 + - - +
374B HIS* 4.9 15.7 - + - +
432B GLN* 2.6 26.2 + - - +
433B ARG* 2.7 65.2 + - + +
434B VAL 3.8 3.6 - - - -
435B GLY* 3.7 17.5 - - - -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 1.3 86.8 - - - +
77B LYS* 1.3 62.1 + - - +
78B VAL* 4.0 4.0 + - + +
328B HIS* 6.4 1.6 - - + -
371B LEU* 2.9 31.9 + - - +
374B HIS* 3.3 39.8 + - + +
375B VAL 2.9 25.3 + - - +
376B VAL* 3.7 17.0 - - + -
432B GLN* 3.5 0.5 - - - -
433B ARG* 3.0 38.1 + - - +
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Residues in contact with LYS 77 (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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76B GLN* 1.3 73.5 - - - +
78B VAL* 1.3 62.9 + - - +
79B LYS 3.6 0.3 + - - -
376B VAL* 3.1 24.0 - - - +
430B GLY* 4.2 19.1 + - - +
431B SER 3.2 6.3 - - - +
432B GLN* 4.0 35.0 - - + +
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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