Contacts of the helix formed by residues 55 - 75 (chain B) in PDB entry 2FGY
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 ASP 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 3.5 3.2 + - - +
54B THR* 1.3 68.3 - - - +
56B LEU* 1.3 58.7 + - - +
57B GLU* 3.6 7.1 + - - +
58B ALA* 3.2 31.6 + - + +
59B ASN* 3.0 30.8 + - - +
187B ARG* 4.7 1.8 - - - +
377B SER* 2.9 16.0 + - - +
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Residues in contact with LEU 56 (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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50B ARG* 3.9 42.0 - - + +
54B THR* 3.4 26.3 + - + +
55B ASP* 1.3 69.3 + - - +
57B GLU* 1.3 74.9 + - + +
59B ASN* 3.2 8.6 + - + +
60B GLU* 3.0 24.4 + - - +
380B ASP* 5.7 0.4 - - - +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 3.4 6.9 + - - +
56B LEU* 1.3 83.1 - - + +
58B ALA* 1.3 64.0 + - - +
60B GLU* 3.3 12.6 + - - +
61B GLN* 3.1 39.5 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 3.2 31.7 + - - +
57B GLU* 1.3 78.8 - - - +
59B ASN* 1.3 63.2 + - - +
61B GLN* 3.3 12.6 + - - +
62B LEU* 2.9 33.7 + - + +
187B ARG* 3.8 16.8 - - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B THR* 3.4 17.5 - - - +
55B ASP 3.0 17.0 + - - +
56B LEU* 3.2 12.2 + - + +
58B ALA* 1.3 74.2 - - - +
60B GLU* 1.3 57.8 + - - +
62B LEU* 3.4 1.5 + - - -
63B GLY* 2.9 24.8 + - - -
187B ARG* 2.9 33.5 + - - -
377B SER* 2.9 24.7 + - - +
380B ASP* 4.2 1.6 - - - +
381B TYR* 3.6 33.1 - - + +
384B ASN* 6.2 0.6 - - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.0 12.7 + - - +
57B GLU* 3.3 17.0 + - - +
59B ASN* 1.3 72.8 - - - +
61B GLN* 1.3 61.2 + - + +
63B GLY* 3.3 2.6 + - - -
64B ARG* 2.9 63.5 + - - +
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.1 29.8 + - - +
58B ALA* 3.9 11.5 - - - +
60B GLU* 1.3 80.0 - - + +
62B LEU* 1.3 58.6 + - + +
64B ARG* 3.5 8.8 + - + +
65B CYS* 3.1 28.4 + - - +
142B PHE* 5.3 1.2 - - - -
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Residues in contact with LEU 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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58B ALA* 2.9 24.6 + - + +
59B ASN* 3.8 4.0 - - - +
61B GLN* 1.3 77.0 - - + +
63B GLY* 1.3 59.1 + - - +
65B CYS* 3.5 5.3 + - + -
66B GLU* 3.0 12.8 + - - +
183B PRO* 3.7 26.2 - - + +
184B TYR* 2.6 57.0 + - + +
187B ARG* 3.3 45.1 - - - +
381B TYR* 3.9 4.7 - - + -
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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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59B ASN 2.9 15.4 + - - -
60B GLU* 3.3 4.0 + - - -
62B LEU* 1.3 74.7 - - - +
64B ARG* 1.3 64.4 + - - +
66B GLU* 3.2 1.0 + - - -
67B ASP* 3.0 31.3 + - - -
381B TYR* 3.5 16.5 - - - -
385B ARG* 3.7 14.0 + - - -
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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
----------------------------------------------------------
60B GLU* 2.9 50.2 + - - +
61B GLN* 3.7 7.9 - - + +
63B GLY* 1.3 74.9 - - - +
65B CYS* 1.3 63.8 + - - +
67B ASP* 4.1 3.7 - - - +
68B SER* 3.0 29.2 + - - -
142B PHE* 4.8 4.9 - - + -
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Residues in contact with CYS 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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61B GLN 3.1 18.1 + - - +
62B LEU* 3.7 8.3 - - + +
63B GLY 3.2 0.2 - - - -
64B ARG* 1.3 77.1 - - - +
66B GLU* 1.3 63.7 + - - +
69B VAL* 3.0 32.1 + - - +
142B PHE* 3.7 46.9 - - + -
184B TYR* 4.1 4.9 - - - +
410B GLU 4.9 5.6 - - - -
413B ILE* 4.0 19.1 - - - -
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 3.0 7.0 + - - +
63B GLY 3.2 2.4 + - - +
65B CYS* 1.3 76.6 - - - +
67B ASP* 1.3 57.7 + - - +
69B VAL* 4.2 0.5 - - - +
70B LYS* 2.8 66.0 + - + +
184B TYR* 3.5 19.1 + - - +
381B TYR* 2.5 42.2 + - - +
385B ARG* 3.6 19.3 + - - +
386B HIS* 5.5 1.2 + - - -
390B TYR* 5.1 9.3 + - - -
394B ASP* 4.6 5.0 - - - +
413B ILE* 3.8 17.4 - - + +
414B ARG* 5.6 4.0 - - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.0 18.4 + - - +
64B ARG* 4.1 3.6 - - - +
66B GLU* 1.3 72.7 - - - +
68B SER* 1.3 61.2 + - - +
70B LYS* 4.0 3.0 - - - +
71B ASN* 3.0 30.8 + - - +
385B ARG* 2.7 40.0 + - - -
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG 3.0 20.2 + - - -
65B CYS 4.0 1.3 - - - -
67B ASP* 1.3 77.8 - - - +
69B VAL* 1.3 63.3 + - - +
71B ASN* 3.3 6.9 + - - +
72B ARG* 3.2 30.5 + - - +
141B GLN* 3.8 21.8 + - - -
142B PHE* 4.1 10.6 - - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B CYS* 3.0 20.6 + - - +
66B GLU 4.2 0.2 - - - +
68B SER* 1.3 77.1 - - - +
70B LYS* 1.3 64.3 + - + +
72B ARG* 3.3 14.2 + - - +
73B PHE* 3.3 17.1 - - + -
138B ALA* 3.9 28.3 - - + -
142B PHE* 3.7 27.8 - - + -
411B VAL* 4.3 4.7 - - + -
413B ILE* 3.8 17.0 - - + -
416B LEU* 3.8 34.1 - - + -
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Residues in contact with LYS 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 GLU* 2.8 49.2 + - + +
67B ASP* 4.3 3.1 - - - +
69B VAL* 1.3 78.9 - - + +
71B ASN* 1.3 56.2 + - - +
73B PHE* 3.4 6.7 + - - +
74B ASP* 2.9 45.5 + - - +
394B ASP* 4.1 15.4 + - - -
400B ARG* 3.7 34.1 - - - +
413B ILE* 4.0 12.3 - - + -
414B ARG* 2.8 31.8 + - - +
415B ASN* 4.3 4.8 - - - +
416B LEU* 4.5 11.4 - - + +
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Residues in contact with ASN 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 ASP 3.0 21.0 + - - +
68B SER* 3.5 7.4 - - - +
69B VAL 3.2 0.2 - - - -
70B LYS* 1.3 74.4 - - - +
72B ARG* 1.3 59.4 + - - +
74B ASP* 4.4 5.3 - - - +
75B ARG* 2.9 61.7 + - - +
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Residues in contact with ARG 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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68B SER* 3.2 18.3 + - - +
69B VAL* 3.3 9.1 + - - +
71B ASN* 1.3 79.3 - - - +
73B PHE* 1.3 59.9 + - + +
75B ARG* 3.6 48.8 + - - +
76B VAL* 3.6 11.4 - - - +
104B LEU* 5.2 1.3 + - - +
134B ALA* 3.6 28.4 - - + +
137B ALA* 3.5 40.2 + - - +
138B ALA* 4.0 11.2 - - - +
141B GLN* 2.9 30.7 + - - +
142B PHE* 6.0 0.2 - - - -
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Residues in contact with PHE 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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69B VAL* 3.3 28.7 - - + -
70B LYS 3.4 5.9 + - - +
72B ARG* 1.3 79.1 - - + +
74B ASP* 1.3 64.4 + - - +
76B VAL* 3.2 23.5 + - - +
77B ILE* 4.4 4.7 + - - +
127B PHE* 6.1 0.2 - - - -
131B THR* 3.6 38.0 + - + -
134B ALA* 4.1 17.9 - - + -
135B LEU* 3.7 26.5 - - + -
138B ALA* 4.7 2.0 - - + -
400B ARG* 3.8 27.8 - - + -
401B TYR* 3.5 30.5 - + - -
416B LEU* 4.0 21.3 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 2.9 28.1 + - - +
71B ASN* 4.2 6.0 - - - +
73B PHE* 1.3 72.1 - - - +
75B ARG* 1.3 58.6 + - - +
77B ILE* 3.2 14.9 + - - +
78B PRO* 3.1 21.5 - - - +
400B ARG* 3.0 49.8 + - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 2.9 43.5 + - - +
72B ARG* 3.6 45.1 + - - +
74B ASP* 1.3 73.1 - - - +
76B VAL* 1.3 67.5 + - - +
77B ILE 3.2 0.6 + - - -
78B PRO* 3.6 11.9 - - + +
79B PHE* 3.4 20.6 + - - +
103B SER* 3.5 24.9 + - - +
104B LEU* 2.9 39.7 + - + +
105B GLY* 4.9 1.2 - - - -
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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