Contacts of the helix formed by residues 59 - 76 (chain A) in PDB entry 4FV3
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 HIS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A SER 6.1 0.7 - - - -
56A PRO 2.8 21.0 + - - +
57A PHE 3.3 0.6 - - - -
58A GLU* 1.3 98.5 + - + +
60A GLN* 1.3 64.6 + - - +
61A THR* 4.4 4.0 - - - +
62A TYR* 3.6 44.2 - + + +
63A CYS* 3.2 12.3 + - - -
338A LYS* 4.2 5.2 - - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 1.3 69.2 - - - +
61A THR* 1.4 61.1 + - - +
63A CYS* 3.3 4.5 + - - +
64A GLN* 2.9 31.4 + - - +
333A LEU 3.9 8.3 + - - -
334A ASP* 3.4 24.0 + - - +
335A ASP* 4.5 0.6 - - - +
336A LEU 2.8 34.3 + - - +
337A PRO* 4.4 1.8 - - + -
338A LYS* 3.9 20.3 - - + +
341A LEU* 3.6 7.4 - - + +
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 3.4 4.4 - - - +
60A GLN* 1.4 77.1 - - - +
62A TYR* 1.3 68.2 + - + +
64A GLN* 3.2 8.8 + - - +
65A ARG* 3.0 51.2 + - + +
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Residues in contact with TYR 62 (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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33A ALA* 4.2 19.3 + - + +
34A TYR* 3.6 58.6 - + + -
55A SER 5.0 1.6 - - - -
56A PRO* 3.6 17.7 - - + +
59A HIS* 3.6 40.7 + + + +
60A GLN 3.4 0.8 - - - -
61A THR* 1.3 85.9 - - + +
63A CYS* 1.4 53.0 + - - +
65A ARG* 3.6 15.0 + - - -
66A THR* 2.6 37.2 + - - -
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Residues in contact with CYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.2 27.8 - - - -
57A PHE* 3.7 28.7 - - - -
59A HIS 3.2 11.2 + - - +
60A GLN* 3.3 8.9 + - - +
62A TYR* 1.4 72.1 - - - +
64A GLN* 1.4 59.6 + - - +
66A THR 3.4 0.5 + - - -
67A LEU* 3.0 30.8 + - - +
338A LYS* 4.0 17.7 - - - -
341A LEU* 3.7 22.7 - - + -
342A LYS 5.0 0.2 - - - -
345A ILE* 3.5 15.0 - - + +
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Residues in contact with GLN 64 (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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60A GLN* 2.9 15.7 + - - +
61A THR* 3.4 11.7 - - - +
63A CYS* 1.4 75.3 - - - +
65A ARG* 1.4 57.2 + - + +
67A LEU* 4.0 4.4 - - - +
68A ARG* 3.0 50.4 + - - +
333A LEU* 4.4 18.8 - - + +
341A LEU* 4.0 9.8 - - + +
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Residues in contact with ARG 65 (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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33A ALA* 5.3 5.7 - - - +
34A TYR* 3.4 32.1 + - - +
61A THR* 3.0 37.0 + - + +
62A TYR* 3.9 19.6 - - - +
64A GLN* 1.4 72.0 - - + +
66A THR* 1.4 64.8 + - - +
68A ARG* 4.0 0.3 - - - +
69A GLU* 3.3 24.9 + - - +
147A ASP* 4.9 4.8 + - - -
165A ASP* 4.8 12.5 + - - -
167A GLY* 3.4 34.6 - - - +
168A LEU* 4.3 34.0 - - + +
186A VAL* 5.5 6.7 - - - +
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Residues in contact with THR 66 (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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34A TYR* 3.3 20.1 + - - -
54A ILE* 3.5 30.3 - - + +
56A PRO* 3.5 6.6 - - + +
62A TYR 2.6 23.2 + - - -
63A CYS 3.6 5.2 - - - -
65A ARG* 1.4 76.8 - - - +
67A LEU* 1.4 57.0 + - - +
69A GLU* 3.4 5.7 + - - +
70A ILE* 3.0 51.8 + - + +
99A VAL* 5.2 3.1 - - + -
101A ILE* 4.8 1.1 - - + -
345A ILE* 4.2 17.9 - - + -
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Residues in contact with LEU 67 (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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63A CYS 3.0 18.3 + - - +
64A GLN* 4.0 3.4 - - - +
66A THR* 1.4 73.2 - - - +
68A ARG* 1.4 59.4 + - - +
70A ILE* 3.3 5.9 + - + +
71A LYS* 2.9 56.7 + - + +
333A LEU* 3.6 30.7 - - + -
341A LEU* 3.9 15.9 - - + +
344A LEU* 3.7 37.2 - - + +
345A ILE* 4.0 13.2 - - + +
348A GLU* 3.8 22.0 - - + -
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Residues in contact with ARG 68 (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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64A GLN* 3.0 31.6 + - - +
65A ARG 4.0 4.3 - - - +
67A LEU* 1.4 74.9 - - - +
69A GLU* 1.3 57.0 + - - +
71A LYS* 3.9 1.6 - - - +
72A ILE* 3.0 38.2 + - + +
166A PHE 4.1 7.9 - - - +
167A GLY 3.9 13.2 + - - +
168A LEU 5.1 1.1 - - - -
169A ALA 3.4 21.9 + - - +
170A ARG* 3.7 20.1 - - - +
329A PHE* 3.8 37.5 - - + -
333A LEU* 3.8 35.1 + - + +
334A ASP* 2.8 34.1 + - - +
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Residues in contact with GLU 69 (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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34A TYR* 5.5 1.7 + - - -
52A LYS* 2.6 33.9 + - - -
54A ILE* 4.9 4.7 - - - +
65A ARG 3.3 16.7 + - - +
66A THR* 3.6 5.3 - - - +
68A ARG* 1.3 76.4 - - - +
70A ILE* 1.3 61.3 + - + +
72A ILE 3.4 0.5 + - - -
73A LEU* 2.9 53.9 + - + +
84A ILE* 4.6 5.0 - - + +
101A ILE* 5.5 1.7 - - - +
103A GLN* 4.8 4.4 + - - -
165A ASP* 3.3 15.2 + - - -
166A PHE* 2.9 43.7 + - - +
167A GLY* 4.2 2.0 - - - +
401A EK6 4.3 1.9 - - - +
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Residues in contact with ILE 70 (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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54A ILE* 5.9 0.4 - - + -
66A THR* 3.0 42.2 + - + +
67A LEU* 3.8 7.4 - - + +
69A GLU* 1.3 74.8 - - + +
71A LYS* 1.3 62.7 + - - +
74A LEU* 3.1 50.3 + - + +
84A ILE* 3.8 10.4 - - + +
87A ILE* 4.1 10.1 - - + -
99A VAL* 4.7 0.9 - - + -
101A ILE* 3.8 30.1 - - + -
345A ILE* 4.6 9.6 - - + -
348A GLU* 4.0 21.1 - - + -
349A THR* 4.2 17.5 - - + -
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Residues in contact with LYS 71 (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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67A LEU* 2.9 38.7 + - + +
68A ARG 3.9 3.4 - - - +
70A ILE* 1.3 75.7 - - - +
72A ILE* 1.3 61.6 + - - +
74A LEU* 3.8 4.4 + - - +
75A ARG* 3.7 13.3 + - - +
327A PHE* 3.6 23.1 - - + -
328A LYS 5.8 0.7 - - - -
329A PHE* 3.8 30.1 - - + +
330A ASP* 4.0 23.8 - - - +
331A MET 5.0 1.8 - - - +
333A LEU* 4.7 11.7 - - + +
344A LEU* 6.2 0.6 - - - +
348A GLU* 3.6 37.9 - - + +
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Residues in contact with ILE 72 (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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68A ARG 3.0 25.5 + - - +
69A GLU* 3.9 3.6 - - - +
71A LYS* 1.3 75.4 - - - +
73A LEU* 1.3 58.1 + - - +
75A ARG* 3.2 4.3 + - - +
76A PHE* 3.1 61.7 + - + -
143A VAL* 4.3 10.8 - - + -
166A PHE* 3.9 17.9 - - + +
169A ALA* 3.6 32.3 - - + +
170A ARG* 4.9 0.7 - - - +
327A PHE* 3.8 27.1 - - + -
329A PHE* 4.0 16.4 - - + -
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Residues in contact with LEU 73 (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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69A GLU* 2.9 45.7 + - + +
72A ILE* 1.3 72.6 - - + +
74A LEU* 1.3 61.3 + - - +
75A ARG 3.3 0.2 - - - -
76A PHE* 3.1 25.3 - - + +
81A ILE* 3.9 9.0 - - + -
82A ILE* 3.5 41.6 - - + +
83A GLY* 5.0 2.3 - - - -
84A ILE* 3.7 27.6 + - + +
103A GLN* 3.8 13.5 - - - +
166A PHE* 3.6 33.4 - - + -
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Residues in contact with LEU 74 (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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70A ILE* 3.1 44.4 + - + +
71A LYS* 4.2 4.5 - - - +
72A ILE 3.3 0.4 - - - -
73A LEU* 1.3 77.4 - - - +
75A ARG* 1.3 58.4 + - - +
76A PHE 4.4 2.3 - - - +
84A ILE* 3.8 28.3 - - + +
87A ILE* 4.4 0.4 - - + -
348A GLU* 3.8 23.8 - - - +
351A ARG* 3.7 38.6 + - - +
352A PHE* 3.5 32.8 - - + -
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Residues in contact with ARG 75 (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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71A LYS 3.7 9.5 + - - +
72A ILE 3.2 9.7 + - - +
74A LEU* 1.3 75.4 - - - +
76A PHE* 1.3 65.5 + - + +
77A ARG* 4.1 0.9 + - - +
137A TYR* 3.9 7.1 + - - -
325A ALA* 4.3 16.8 + - - +
326A PRO 2.8 30.4 + - - -
327A PHE* 3.7 34.2 - - + +
328A LYS* 3.8 20.6 + - - +
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Residues in contact with PHE 76 (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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72A ILE* 3.1 41.9 + - + +
73A LEU* 3.1 22.0 + - + +
74A LEU 3.4 2.8 - - - +
75A ARG* 1.3 86.2 - - + +
77A ARG* 1.3 62.5 + - - +
78A HIS 4.3 0.2 - - - -
81A ILE* 4.1 28.0 - - + -
82A ILE 5.7 0.6 - - - +
83A GLY* 5.7 3.6 - - - -
137A TYR* 3.6 20.0 - + + -
138A ILE* 4.0 27.4 - - + -
141A ALA* 3.6 32.3 - - + -
143A VAL* 3.9 17.0 - - + -
166A PHE* 4.1 6.1 - + - -
323A ALA* 5.3 1.1 - - + -
327A PHE* 4.8 8.7 - + - -
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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
------------------------------------------------------------
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