Contacts of the helix formed by residues 62 - 76 (chain B) in PDB entry 3SFX
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 ARG 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 4.8 5.3 - - - +
58B TYR 3.3 25.1 + - - -
59B SER* 4.5 2.4 - - - +
60B GLY 3.3 15.8 + - - +
61B LEU* 1.3 68.6 - - - +
63B LYS* 1.3 63.5 - - - +
65B GLU* 3.1 27.9 + - + +
66B HIS* 3.1 27.8 + - + +
385B LEU 4.6 2.8 + - - -
386B VAL 5.7 1.6 + - - -
389B GLN* 2.8 41.7 + - - +
390B GLN 2.9 28.9 + - - -
391B ASP* 4.4 0.8 - - - +
392B PRO* 3.8 34.7 - - - +
523B 3FX 3.1 30.5 - - - +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.0 32.2 + - + +
62B ARG* 1.3 71.6 - - - +
64B GLN* 1.3 61.0 + - + +
66B HIS* 3.4 9.0 + - - +
67B THR* 2.8 34.4 + - - +
102B LEU* 3.3 49.3 + - + +
103B GLY* 5.2 1.0 - - - -
491B ASP 4.1 16.6 + - - +
493B ARG 3.4 23.8 + - - -
494B ILE* 4.2 9.9 - - - +
523B 3FX 3.5 2.6 + - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 1.3 77.6 - - + +
65B GLU* 1.3 60.0 + - - +
67B THR* 3.3 8.3 + - - -
68B GLN* 3.0 44.1 + - - +
523B 3FX 3.0 36.1 + - + +
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Residues in contact with GLU 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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62B ARG* 3.5 35.2 + - + +
64B GLN* 1.3 77.1 - - - +
66B HIS* 1.3 58.3 + - - +
68B GLN* 3.3 15.8 + - - +
69B PHE* 2.9 28.6 + - - +
390B GLN 4.7 1.2 - - - +
391B ASP 4.2 3.8 - - - +
392B PRO* 3.8 4.5 - - - +
393B GLY* 2.8 34.7 + - - -
394B SER 4.5 6.6 + - - +
395B THR 3.8 1.5 - - - +
396B GLY* 3.7 24.5 + - - +
523B 3FX 3.0 32.1 + - + +
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.0 12.1 - - + +
62B ARG* 3.1 26.6 + - + -
63B LYS* 3.8 7.2 - - - +
65B GLU* 1.3 73.8 - - + +
67B THR* 1.3 65.4 + - - +
69B PHE* 3.3 3.3 + - - +
70B LEU* 3.1 27.7 + - - +
102B LEU* 4.0 21.5 - - + -
389B GLN* 2.8 36.8 + - + +
390B GLN* 4.6 2.5 - - + -
396B GLY* 4.4 3.8 - - - -
397B GLY* 2.9 50.1 + - - +
398B LEU* 3.8 24.5 - - + +
411B THR* 5.2 3.4 - - + -
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Residues in contact with THR 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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63B LYS 2.8 25.0 + - - -
64B GLN* 3.5 9.4 - - - -
66B HIS* 1.3 74.8 - - - +
68B GLN* 1.3 63.3 + - + +
70B LEU* 3.2 4.7 + - - +
71B ALA* 3.0 24.7 + - + +
99B LEU* 4.0 23.0 - - + +
102B LEU* 4.1 7.6 - - - +
104B VAL* 3.5 34.3 - - + +
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Residues in contact with GLN 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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64B GLN* 3.0 32.5 + - - +
65B GLU* 3.3 16.0 + - - +
67B THR* 1.3 76.7 - - + +
69B PHE* 1.3 63.3 + - - +
71B ALA* 3.3 14.9 + - - +
72B SER* 3.2 18.2 + - - -
395B THR 5.4 1.6 - - - +
523B 3FX 6.3 1.0 - - - -
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Residues in contact with PHE 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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65B GLU 2.9 10.6 + - - +
66B HIS 3.4 8.5 - - - +
68B GLN* 1.3 76.9 - - - +
70B LEU* 1.3 65.3 + - + +
72B SER* 2.9 20.2 + - - -
73B SER* 3.0 12.5 + - - -
395B THR* 3.4 26.8 + - - +
396B GLY 3.3 17.7 - - - -
397B GLY* 3.6 18.8 - - - +
406B PRO* 3.8 15.9 - - + -
407B ASP* 3.7 32.1 - - - -
408B GLN* 4.0 18.6 - - + -
411B THR* 3.6 19.3 - - - -
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Residues in contact with LEU 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 HIS 3.1 17.2 + - - +
67B THR 3.2 4.4 + - - +
69B PHE* 1.3 83.4 - - + +
71B ALA* 1.3 63.2 + - - +
73B SER* 3.0 14.1 + - - -
74B PHE* 3.1 14.7 + - - +
94B TRP 4.5 2.5 - - - +
95B THR* 3.9 34.9 - - + +
98B SER* 3.4 28.0 - - - -
99B LEU* 4.0 26.9 - - + -
102B LEU* 4.0 9.6 - - + -
408B GLN* 4.6 11.7 - - + -
411B THR* 4.0 24.9 - - + -
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Residues in contact with ALA 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 THR* 3.0 19.5 + - + +
68B GLN* 3.3 9.8 + - - +
70B LEU* 1.3 76.5 - - - +
72B SER* 1.3 56.1 + - - +
74B PHE* 2.7 36.4 + - + +
75B PHE* 3.6 22.1 + - + -
99B LEU* 5.9 0.4 - - - +
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Residues in contact with SER 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 GLN 3.2 10.4 + - - -
69B PHE* 2.9 20.8 + - - -
71B ALA* 1.3 76.5 - - - +
73B SER* 1.3 62.4 + - - +
74B PHE 3.6 0.2 + - - -
75B PHE 4.2 0.2 + - - -
76B GLN* 3.0 26.2 + - - +
78B PRO* 5.8 0.3 - - - +
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Residues in contact with SER 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 VAL* 4.1 6.4 - - - +
69B PHE 3.0 12.9 + - - -
70B LEU* 3.0 21.0 + - - -
72B SER* 1.3 81.3 + - - +
74B PHE* 1.3 62.6 + - - +
75B PHE 3.5 0.6 + - - -
76B GLN 4.2 0.3 + - - -
77B LEU* 3.3 37.2 - - - +
81B PHE* 5.1 0.2 - - - -
91B LEU* 6.0 0.4 - - - -
95B THR* 4.6 3.6 + - - -
408B GLN* 2.9 39.8 + - - +
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Residues in contact with PHE 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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30A VAL* 3.7 29.0 - - + -
31A VAL* 2.9 34.5 + - + +
70B LEU 3.1 10.3 + - - +
71B ALA* 2.7 29.9 + - - +
73B SER* 1.3 71.6 - - - +
75B PHE* 1.4 86.8 + + + +
95B THR* 3.7 29.8 - - + -
96B VAL* 4.6 4.3 - - + -
99B LEU* 3.9 7.9 - - + -
106B LEU* 3.6 34.5 - - + -
110B THR* 3.8 17.0 - - + -
114B VAL* 4.1 9.6 - - + -
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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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32A PRO* 3.5 19.1 - - - +
71B ALA* 3.6 25.4 + - + -
72B SER 4.2 0.4 + - - -
74B PHE* 1.4 117.3 - + + +
76B GLN* 1.3 66.7 + - - +
106B LEU* 6.2 0.2 - - + -
110B THR* 4.3 11.4 - - + -
113B ARG* 3.3 39.7 + - - +
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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
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32A PRO* 3.8 11.3 - - + +
34A MET* 3.4 46.9 - - + +
72B SER 3.0 20.4 + - - +
74B PHE 3.8 1.0 - - - -
75B PHE* 1.3 80.3 - - - +
77B LEU* 1.3 64.1 + - - +
78B PRO* 4.1 4.3 - - - +
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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