Contacts of the helix formed by residues 65 - 78 (chain B) in PDB entry 4UFT
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 SER 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B VAL* 1.3 77.8 - - - +
66B GLY* 1.3 67.2 + - - +
67B PRO* 4.3 6.9 - - - +
68B LYS* 3.2 33.1 + - - +
69B LEU* 3.3 21.5 + - - +
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Residues in contact with GLY 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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65B SER* 1.3 73.0 - - - +
67B PRO* 1.3 60.5 - - - +
69B LEU* 3.0 6.5 + - - +
70B THR* 2.8 35.3 + - - -
222B ARG* 3.4 34.4 + - - -
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Residues in contact with PRO 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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33B HIS* 5.8 8.7 - - + +
34B ILE* 5.4 7.2 - - + -
35B ILE* 4.2 31.1 - - + +
36B ILE 4.8 4.3 + - - +
65B SER* 4.1 7.2 - - - +
66B GLY* 1.3 89.1 - - - +
68B LYS* 1.3 56.5 + - - +
70B THR* 4.0 8.1 - - - -
71B GLY* 2.8 28.8 + - - -
222B ARG* 4.4 1.3 - - - +
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Residues in contact with LYS 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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58B LEU* 3.7 23.6 - - + +
64B VAL* 5.1 2.7 - - + -
65B SER* 3.2 32.3 + - - +
66B GLY 3.2 0.4 - - - -
67B PRO* 1.3 78.8 - - - +
69B LEU* 1.3 60.6 + - - +
71B GLY* 4.6 0.2 - - - -
72B ALA* 3.4 22.3 + - - +
129B GLN* 3.0 29.9 + - - +
130B TYR* 4.1 32.8 + - + +
133B HIS* 3.6 28.3 + - + +
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Residues in contact with LEU 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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58B LEU* 4.9 4.3 - - - +
59B ILE* 3.8 47.1 - - + +
64B VAL* 4.9 15.9 - - + +
65B SER 3.3 14.6 + - - +
66B GLY* 3.0 4.5 + - - +
68B LYS* 1.3 78.6 - - - +
70B THR* 1.3 58.6 + - - +
72B ALA* 3.4 2.6 + - - +
73B LEU* 3.0 35.2 + - + +
218B VAL* 4.5 18.2 - - + +
219B VAL* 5.8 1.8 - - + -
222B ARG* 3.8 37.7 - - + -
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Residues in contact with THR 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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35B ILE* 4.2 12.1 - - + -
66B GLY 2.8 21.8 + - - -
67B PRO* 3.8 8.5 - - - +
69B LEU* 1.3 74.7 - - - +
71B GLY* 1.3 62.7 + - - +
73B LEU* 3.2 4.3 + - - +
74B ILE* 3.0 39.3 + - + +
222B ARG* 3.2 25.9 + - - +
226B ASP* 4.2 12.7 + - - +
229B LEU* 4.1 23.3 - - + +
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Residues in contact with GLY 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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35B ILE* 3.6 18.1 - - - +
36B ILE 3.8 16.2 - - - -
37B VAL* 4.0 7.5 - - - +
38B PRO* 3.9 7.4 - - - +
67B PRO 2.8 20.3 + - - -
70B THR* 1.3 73.6 - - - +
72B ALA* 1.3 56.6 - - - +
74B ILE* 3.4 2.9 + - - +
75B GLY* 2.9 26.0 + - - -
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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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36B ILE 4.8 0.2 + - - -
38B PRO* 4.8 4.9 - - + +
55B LEU* 3.7 17.3 - - + +
58B LEU* 4.0 18.6 - - + -
59B ILE* 4.0 19.7 - - + +
68B LYS 3.4 20.4 + - - +
69B LEU* 3.4 6.2 + - - +
70B THR 3.2 0.2 - - - -
71B GLY* 1.3 74.7 - - - +
73B LEU* 1.3 59.3 + - - +
75B GLY 4.4 0.2 - - - +
76B ILE* 2.8 34.2 + - - +
130B TYR* 5.2 0.8 + - - +
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Residues in contact with LEU 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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59B ILE* 4.6 7.1 - - + +
69B LEU* 3.0 22.8 + - + +
70B THR 3.2 5.6 + - - +
72B ALA* 1.3 76.5 - - - +
74B ILE* 1.3 63.4 + - + +
76B ILE* 3.3 12.9 - - + +
77B LEU* 3.3 23.2 + - + +
174B ILE* 5.1 13.0 - - + -
219B VAL* 4.0 33.2 - - + +
222B ARG* 5.2 7.2 - - + -
223B ILE* 4.7 4.7 - - + -
229B LEU* 3.8 41.7 - - + -
233B MET* 4.6 15.3 - - + -
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Residues in contact with ILE 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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35B ILE* 4.2 14.4 - - + -
37B VAL* 4.1 18.4 - - + -
70B THR* 3.0 38.5 + - + +
71B GLY* 3.7 5.4 - - - +
73B LEU* 1.3 80.4 - - + +
75B GLY* 1.3 58.8 + - - +
77B LEU* 3.3 4.9 + - - +
78B SER* 2.9 34.8 + - - +
88B ILE* 4.9 4.9 - - + -
97B VAL* 6.3 0.2 - - + -
99B ILE* 4.3 16.6 - - + -
229B LEU* 5.5 7.4 - - + -
232B PHE* 3.9 44.9 - - + -
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Residues in contact with GLY 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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37B VAL* 4.1 14.1 - - - +
38B PRO* 4.1 13.4 - - - +
55B LEU* 3.9 10.3 - - - +
71B GLY 2.9 16.7 + - - -
72B ALA 3.8 0.9 - - - -
74B ILE* 1.3 78.2 - - - +
76B ILE* 1.3 60.7 + - - +
78B SER* 3.2 23.7 - - - +
79B LEU* 3.9 10.9 - - - +
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Residues in contact with ILE 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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52B LEU* 3.7 36.3 - - + +
55B LEU* 3.5 29.9 - - + +
56B VAL* 4.5 6.7 - - + +
59B ILE* 4.1 15.0 - - + -
72B ALA 2.8 23.3 + - - +
73B LEU* 3.3 18.2 - - + +
75B GLY* 1.3 71.7 - - - +
77B LEU* 1.3 65.6 + - + +
79B LEU* 4.1 11.5 - - + +
167B LEU* 4.6 1.0 - - - +
170B ILE* 4.5 24.2 - - + -
171B LEU* 3.3 18.1 - - + +
174B ILE* 5.6 10.1 - - + -
215B TRP* 6.0 1.1 - - + -
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Residues in contact with LEU 77 (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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73B LEU* 3.3 18.6 + - + +
74B ILE* 3.3 5.8 + - - +
75B GLY 3.2 0.4 - - - -
76B ILE* 1.3 86.1 - - + +
78B SER* 1.3 63.1 + - - +
79B LEU 3.0 6.9 + - - -
80B PHE* 3.3 22.9 - - + -
171B LEU* 3.5 22.8 - - + +
174B ILE* 4.5 18.6 - - + -
175B TRP* 3.6 48.5 - - + +
232B PHE* 4.7 13.9 - - + -
233B MET* 5.2 9.4 - - + -
236B LEU* 4.2 18.8 - - + -
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Residues in contact with SER 78 (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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37B VAL* 5.2 0.2 - - - +
39B ILE* 6.0 0.3 - - - +
40B PRO* 5.3 1.6 - - - +
74B ILE* 2.9 20.1 + - - +
75B GLY* 3.2 12.2 + - - +
77B LEU* 1.3 75.9 - - - +
79B LEU* 1.3 63.0 + - - +
80B PHE* 3.8 9.2 - - - -
81B VAL* 5.3 4.7 - - - -
84B PRO* 4.4 18.4 - - - +
87B LEU* 5.0 10.5 - - - -
88B ILE* 4.2 22.1 - - - +
232B PHE* 4.8 14.6 - - - -
236B LEU* 6.3 2.0 - - - -
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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