Contacts of the helix formed by residues 60 - 73 (chain B) in PDB entry 3NYN
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B SER* 2.9 46.4 + - - +
56B LEU* 4.0 12.7 - - - +
58B GLU 3.5 1.4 - - - +
59B ARG* 1.3 76.9 - - + +
61B PRO* 1.3 59.1 - - - -
63B GLY* 2.6 34.3 + - - +
64B ARG* 2.9 9.9 + - - -
170B PHE* 3.6 13.3 - - - -
174B LYS* 2.9 29.1 + - - +
508B PRO* 5.2 5.2 - - + -
509B ILE* 4.9 10.1 - - + -
512B GLN* 2.8 35.1 + - - +
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Residues in contact with PRO 61 (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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58B GLU 5.4 0.7 - - - +
59B ARG 3.0 13.7 - - - +
60B GLN* 1.3 80.0 - - - -
62B ILE* 1.3 61.9 + - - +
64B ARG* 2.9 10.2 + - + +
65B LEU* 2.7 34.8 + - + +
509B ILE* 3.8 25.1 - - + +
512B GLN* 3.3 14.8 - - + +
513B ASN* 3.3 28.0 - - - +
516B VAL* 5.0 4.7 - - + -
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Residues in contact with ILE 62 (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 GLN 3.0 1.2 + - - -
61B PRO* 1.3 73.8 - - - +
63B GLY* 1.3 68.6 + - - +
64B ARG 3.0 0.5 + - - -
65B LEU* 3.0 6.4 + - - +
66B LEU* 2.7 42.2 + - + +
170B PHE* 4.4 5.8 - - + -
173B TRP* 4.2 29.4 - - + -
511B TRP* 4.7 3.6 - - + -
512B GLN* 3.0 42.8 + - + +
515B MET* 4.5 7.6 - - + -
516B VAL* 4.1 14.1 - - + -
521B PHE* 3.7 39.0 - - + -
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Residues in contact with GLY 63 (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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56B LEU 3.2 23.1 - - - +
60B GLN* 2.6 15.4 + - - -
62B ILE* 1.3 73.9 - - - +
64B ARG* 1.3 54.8 + - - -
66B LEU* 3.4 1.9 + - - +
67B PHE* 2.8 29.3 + - - +
161B TYR* 3.7 2.7 + - - -
170B PHE* 3.5 27.5 - - - -
512B GLN* 3.9 0.8 + - - -
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Residues in contact with ARG 64 (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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535A PRO* 3.8 17.8 - - + +
537A LEU 3.2 23.8 + - - -
538A ASP* 3.3 6.7 + - - +
539A TRP* 3.2 31.6 + - - +
56B LEU 3.9 1.0 + - - -
57B CYS* 3.6 29.5 - - - +
58B GLU* 3.7 18.1 + - - +
60B GLN 2.9 9.3 + - - +
61B PRO* 2.9 12.9 + - + +
63B GLY* 1.3 71.3 - - - +
65B LEU* 1.3 67.3 + - - +
67B PHE* 2.7 4.6 + - - +
68B ARG* 2.7 36.1 + - + +
85B ASP* 4.6 8.9 + - - -
583B BU3 2.7 38.6 + - - +
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Residues in contact with LEU 65 (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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531A GLY 5.5 0.2 - - - +
532A SER* 3.5 30.1 - - - +
533A VAL 4.6 0.4 - - - +
534A PRO* 3.8 21.8 - - + -
535A PRO* 4.4 10.8 - - + -
61B PRO* 2.7 27.8 + - + +
62B ILE* 3.5 7.0 - - - +
64B ARG* 1.3 71.9 - - - +
66B LEU* 1.3 58.4 + - - +
68B ARG* 3.1 12.3 + - - +
69B GLU* 2.7 36.9 + - - +
516B VAL* 3.9 36.6 - - + -
521B PHE* 4.2 23.3 - - + -
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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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527A PHE* 4.7 1.6 - - + -
62B ILE* 2.7 36.7 + - + +
63B GLY 3.6 3.8 - - - +
65B LEU* 1.3 73.6 - - - +
67B PHE* 1.3 61.4 + - - +
69B GLU* 3.3 13.8 + - - +
70B PHE* 3.0 21.7 + - - +
161B TYR* 3.9 12.8 - - + +
166B TYR* 3.7 22.3 - - + +
169B ARG* 4.3 4.9 - - + -
170B PHE* 3.3 46.0 - - + +
173B TRP* 4.1 6.5 - - + -
521B PHE* 4.3 3.6 - - + -
525B ASN* 3.9 27.8 - - - +
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Residues in contact with PHE 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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53B TYR* 4.1 19.3 - + - -
57B CYS* 3.6 24.7 - - + -
63B GLY 2.8 12.7 + - - +
64B ARG* 2.7 15.1 + - - +
66B LEU* 1.3 68.7 - - - +
68B ARG* 1.3 65.9 + - - +
70B PHE* 2.9 17.8 + + - +
71B CYS* 3.0 36.1 + - - -
153B LEU* 4.6 11.4 - - + -
157B PRO* 4.2 11.7 - - + -
158B PHE* 4.5 14.1 - - - -
161B TYR* 3.5 47.9 - + + -
583B BU3 4.0 26.2 - - + -
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Residues in contact with ARG 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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531A GLY* 4.0 16.1 + - - +
533A VAL 3.9 13.1 + - - -
535A PRO* 3.4 36.7 - - - +
64B ARG* 2.7 32.0 + - + +
65B LEU* 3.3 14.6 - - - +
67B PHE* 1.3 71.2 - - - +
69B GLU* 1.3 64.5 + - - +
71B CYS* 3.0 12.3 + - - +
72B ALA* 2.9 21.7 + - - +
81B VAL* 3.4 18.4 - - + +
85B ASP* 2.6 46.1 + - - -
583B BU3 3.7 31.6 + - + -
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Residues in contact with GLU 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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527A PHE* 4.2 4.2 - - - -
528A GLY* 3.4 31.6 + - - +
530A ASP* 3.7 14.0 - - - +
531A GLY 3.3 19.5 - - - +
532A SER* 3.3 17.6 - - - -
65B LEU* 2.7 23.6 + - - +
66B LEU* 3.5 16.3 - - - +
68B ARG* 1.3 74.2 - - - +
70B PHE* 1.3 63.6 + - - +
72B ALA* 3.2 17.4 + - - +
73B THR* 3.7 8.1 + - - +
166B TYR* 3.8 12.2 + - + -
521B PHE* 3.8 13.3 - - - -
522B GLN* 4.6 0.5 - - - +
525B ASN* 3.5 20.9 + - - -
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Residues in contact with PHE 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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66B LEU 3.0 12.0 + - - +
67B PHE* 2.9 17.5 + + - +
69B GLU* 1.3 78.9 - - - +
71B CYS* 1.3 65.9 + - - +
73B THR* 2.9 31.5 + - - +
74B ARG* 4.1 15.8 + - - +
77B LEU* 4.0 20.2 - - + -
157B PRO 3.9 8.7 - - - -
160B ASP* 3.8 13.2 - - + -
161B TYR* 3.5 45.1 - + + -
164B SER* 3.8 26.5 - - - -
166B TYR* 3.8 26.0 - + + -
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Residues in contact with CYS 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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67B PHE* 3.0 52.4 + - - -
68B ARG* 3.0 7.6 + - - +
70B PHE* 1.3 81.7 - - - +
72B ALA* 1.3 58.7 + - - +
74B ARG 2.9 29.3 + - - +
77B LEU* 3.7 29.1 - - + +
78B SER* 3.3 5.5 + - - -
81B VAL* 4.0 25.6 - - + -
153B LEU* 5.2 5.2 - - - -
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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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530A ASP* 3.9 31.9 - - + +
531A GLY* 4.0 12.6 - - - +
68B ARG 2.9 11.2 + - - +
69B GLU 3.2 14.4 - - - +
70B PHE 3.0 0.6 - - - -
71B CYS* 1.3 77.4 - - - +
73B THR* 1.3 60.1 + - - +
74B ARG* 3.3 2.0 + - - -
75B PRO* 5.0 0.5 - - - +
78B SER* 4.3 17.7 - - - +
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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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31A ARG* 5.9 4.5 - - - +
530A ASP* 6.0 2.5 - - + -
69B GLU 3.8 3.1 - - - +
70B PHE* 2.9 23.4 + - + +
72B ALA* 1.3 76.5 - - - +
74B ARG* 1.3 73.8 + - - +
75B PRO* 4.0 5.9 - - - +
166B TYR* 3.1 37.5 - - + +
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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