Contacts of the strand formed by residues 65 - 77 (chain D) in PDB entry 3RIK
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D GLY* 1.3 71.5 - - - +
66D LEU* 1.3 65.1 + - - +
67D LEU* 4.0 17.0 - - + -
439D SER* 3.8 15.7 - - - +
440D GLN* 3.7 44.0 + - + +
442D ASN* 3.7 31.6 - - + +
444D LEU* 4.1 22.0 - - + -
468D VAL* 4.2 11.2 - - + -
469D PRO 3.9 13.4 + - - +
470D LEU* 3.5 10.1 - - + -
471D THR* 3.1 26.0 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D HIS* 4.2 10.1 - - + +
64D GLY 4.1 5.4 - - - +
65D LEU* 1.3 74.6 - - - +
67D LEU* 1.3 62.5 + - - +
68D THR* 3.7 20.1 + - - +
437D VAL 3.5 1.4 - - - +
438D ALA* 3.4 2.8 - - - -
439D SER* 2.7 52.5 + - - +
471D THR* 3.4 35.7 - - + +
473D LYS* 4.3 14.8 - - + -
479D PHE* 4.1 19.7 - - + -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 4.0 17.7 - - + -
66D LEU* 1.3 78.2 - - - +
68D THR* 1.3 56.2 + - - +
436D LEU* 3.7 22.0 - - + -
437D VAL 3.2 3.6 - - - +
438D ALA* 3.7 23.3 - - + +
442D ASN* 5.0 2.9 - - - +
444D LEU* 5.3 6.3 - - + -
446D ALA* 4.0 26.9 - - + -
458D VAL* 5.4 0.7 - - + -
460D VAL* 4.7 4.7 - - + -
470D LEU* 3.7 29.4 - - + -
471D THR 2.8 11.7 + - - +
472D ILE* 3.1 16.5 - - + +
473D LYS 2.7 30.4 + - - -
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 3.7 23.7 + - - +
67D LEU* 1.3 73.9 - - - +
69D LEU* 1.3 76.3 + - - +
70D GLN* 3.6 9.3 + - + +
436D LEU* 3.2 5.5 - - - -
437D VAL* 2.7 44.9 + - - +
439D SER* 6.1 0.2 - - - -
473D LYS* 3.6 29.8 - - + +
475D PRO* 4.9 4.5 - - + -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU 3.9 1.4 + - - -
68D THR* 1.3 78.7 - - - +
70D GLN* 1.3 62.2 + - - +
71D PRO* 3.1 20.2 - - + +
434D VAL* 4.1 12.1 - - + -
435D GLY 3.6 2.0 - - - -
436D LEU* 4.0 5.5 - - + +
448D ALA* 3.6 30.5 - - + -
449D LEU 5.5 1.3 - - - +
450D MET* 5.9 3.1 - - + -
456D ALA* 4.8 7.4 - - + -
457D VAL 5.7 0.2 - - - +
458D VAL* 4.4 12.8 - - + -
472D ILE* 5.0 3.4 - - + -
473D LYS 2.9 18.1 + - - +
474D ASP* 3.6 35.4 - - + +
475D PRO* 3.7 11.4 - - - +
494D TRP* 4.3 8.5 - - + -
496D ARG* 4.1 13.5 - - - +
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Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR* 3.8 13.8 - - + +
69D LEU* 1.3 77.4 - - - +
71D PRO* 1.3 55.8 - - - +
72D GLU* 2.9 15.7 + - + -
73D GLN* 2.9 44.5 + - + +
434D VAL* 3.9 1.1 - - - +
435D GLY* 2.8 35.3 + - - +
437D VAL* 3.3 32.6 - - - +
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Residues in contact with PRO 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.1 22.4 - - + +
70D GLN* 1.3 83.7 - - - +
72D GLU* 1.3 73.6 + - + +
73D GLN 3.4 0.2 - - - -
74D LYS* 3.1 30.3 + - - +
434D VAL* 4.2 16.7 - - + +
450D MET* 4.5 6.9 - - - +
475D PRO* 4.3 15.7 - - + -
496D ARG* 3.4 38.8 - - - +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLN* 2.9 1.8 + - + -
71D PRO* 1.3 96.8 - - + +
73D GLN* 1.3 62.7 + - + +
74D LYS* 3.3 25.8 + - - +
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Residues in contact with GLN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLN* 2.9 36.6 + - + +
72D GLU* 1.3 77.5 - - + +
74D LYS* 1.3 62.8 + - - +
75D PHE* 3.5 25.3 - - + -
434D VAL* 3.2 8.6 - - - -
435D GLY* 3.1 25.3 + - - +
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PRO 3.1 25.9 + - - +
72D GLU* 3.3 23.5 + - - +
73D GLN* 1.3 74.9 - - - +
75D PHE* 1.3 67.6 + - - +
432D GLN* 3.5 32.3 + - - +
433D ARG 3.9 2.5 - - - -
434D VAL* 4.5 6.3 - - + +
450D MET* 3.8 28.3 - - - +
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Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D GLN* 3.5 38.8 - - + -
74D LYS* 1.3 76.4 - - - +
76D GLN* 1.3 77.4 + - - +
77D LYS* 3.7 0.5 + - - +
374D HIS* 4.2 20.6 - + - +
432D GLN* 2.7 27.9 + - - -
433D ARG* 2.7 60.8 + - - +
434D VAL 4.0 1.6 - - - -
435D GLY* 3.9 15.5 - - - -
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 1.3 93.3 - - - +
77D LYS* 1.3 73.3 + - - +
78D VAL* 4.8 2.9 - - + +
328D HIS* 6.1 1.6 - - - +
371D LEU* 3.0 34.8 + - - +
374D HIS* 3.5 39.2 + - + +
375D VAL 2.9 23.8 + - - +
376D VAL* 3.9 6.7 - - + -
432D GLN* 3.5 0.7 - - - -
433D ARG* 3.1 38.8 + - + +
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE 3.7 0.4 + - - +
76D GLN* 1.3 78.0 - - - +
78D VAL* 1.3 61.1 + - - +
376D VAL* 3.2 27.2 - - - +
430D GLY* 4.3 21.4 + - - +
431D SER 3.3 7.9 - - - +
432D GLN* 4.3 28.7 + - + +
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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