Contacts of the helix formed by residues 58 - 72 (chain D) in PDB entry 3EXF
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.2 26.0 + - - +
172A GLN* 3.8 0.7 - - - +
177C GLU* 3.1 30.4 - - - +
180C ASN* 4.9 1.0 + - - -
181C MET* 3.3 26.5 - - - +
56D PRO* 3.0 13.7 + - - +
57D ILE* 1.3 76.6 - - - +
59D GLU* 1.3 64.6 + - - +
61D GLY 3.0 1.0 + - - -
62D PHE* 3.0 23.7 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.4 7.6 + - - +
1003A TPP 2.8 36.0 + - - +
28D GLU* 2.3 34.0 - - - +
57D ILE* 4.1 2.8 - - - +
58D SER* 1.3 69.6 - - - +
60D MET* 1.3 73.4 + - - +
61D GLY 2.8 1.0 + - - -
62D PHE* 3.6 13.3 - - + -
63D ALA* 3.0 21.7 + - - +
80D PHE* 4.2 11.2 - - + -
81D MET 5.2 0.3 + - - -
85D PHE* 3.4 30.2 - - + +
88D GLN* 3.3 22.5 + - + +
89D ALA* 4.2 7.9 - - + -
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Residues in contact with MET 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B MET* 5.4 7.4 - - + -
88B GLN* 4.1 36.8 - - + +
143C PRO* 4.8 0.6 - - + +
174C GLN* 3.5 43.1 - - + +
177C GLU* 3.3 16.8 + - - +
59D GLU* 1.3 82.6 - - - +
61D GLY* 1.3 57.7 + - - +
63D ALA* 3.5 0.7 + - - +
64D GLY* 3.1 21.3 + - - -
88D GLN* 3.3 32.2 + - + +
89D ALA* 4.1 8.7 - - - +
91D ASP* 5.1 6.5 - - - +
92D GLN* 3.6 26.5 + - + +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.9 15.6 - - - +
174C GLN* 5.0 0.2 - - - -
177C GLU* 2.7 35.5 + - - -
178C ALA 5.0 1.5 + - - -
181C MET* 3.9 6.5 - - - -
58D SER 3.5 1.1 - - - -
59D GLU 2.8 1.6 + - - -
60D MET* 1.3 75.1 - - - +
62D PHE* 1.3 58.0 + - - +
64D GLY 3.8 0.8 + - - -
65D ILE* 3.2 30.7 + - - +
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Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C MET* 3.9 12.7 - - - +
26D LEU* 4.1 12.6 - - + +
27D GLY* 4.2 5.2 - - - -
28D GLU* 3.5 24.7 - - + -
55D THR* 3.3 44.0 - - + -
56D PRO 3.7 8.5 - - - -
58D SER* 3.0 41.2 + - - -
59D GLU* 3.6 13.5 - - + -
61D GLY* 1.3 76.0 - - - +
63D ALA* 1.3 69.2 + - - +
64D GLY 3.1 0.7 - - - -
65D ILE* 3.6 5.9 - - + +
66D ALA* 2.8 24.6 + - - +
78D CYS* 4.3 9.6 - - - -
79D GLU 3.7 23.3 - - - -
80D PHE* 4.3 13.5 - + - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU 3.0 16.6 + - - +
60D MET 3.6 2.5 - - - +
62D PHE* 1.3 80.4 - - - +
64D GLY* 1.3 65.7 + - - +
66D ALA* 3.0 2.6 + - - +
67D VAL* 2.8 24.5 + - - +
78D CYS* 4.4 13.2 - - - -
80D PHE* 4.2 11.7 - - + -
89D ALA* 3.5 23.8 - - + -
92D GLN* 3.7 13.9 - - + -
93D VAL* 5.4 0.4 - - + +
114D PHE* 4.6 7.9 - - + -
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Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.8 20.2 - - - -
144C LEU* 3.6 9.8 - - - -
60D MET 3.1 8.3 + - - -
62D PHE 3.1 0.4 - - - -
63D ALA* 1.3 80.4 - - - +
65D ILE* 1.3 62.2 + - - +
67D VAL* 3.3 3.9 + - - +
68D GLY 3.1 18.0 + - - -
92D GLN* 3.4 28.0 - - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.7 17.0 + - + +
146C ALA* 3.8 21.5 - - + +
147C GLY* 3.5 9.7 - - - +
150C LEU* 4.1 23.6 - - + -
178C ALA* 4.9 5.4 - - - -
181C MET* 3.9 35.7 - - + -
185C TRP* 4.2 17.0 - - + -
187C LEU* 5.5 1.8 - - + -
24D PHE* 6.1 0.2 - - + -
26D LEU* 4.3 11.9 - - + -
61D GLY 3.2 22.7 + - - +
62D PHE* 3.1 7.7 + - - +
64D GLY* 1.3 74.8 - - - +
66D ALA* 1.3 57.9 + - - +
68D GLY 3.4 0.3 + - - -
69D ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 5.4 0.7 - - - -
26D LEU* 4.1 13.7 - - + -
62D PHE 2.8 12.6 + - - +
63D ALA 3.3 8.7 - - - +
65D ILE* 1.3 76.0 - - - +
67D VAL* 1.3 63.8 + - - +
68D GLY 3.0 5.1 + - - -
69D ALA* 3.3 5.5 + - - +
70D ALA* 3.0 20.3 + - - +
76D PRO* 3.4 13.1 - - + +
78D CYS* 4.0 17.7 - - + -
112D ILE* 3.4 21.1 - - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 3.6 21.8 - - + -
63D ALA 2.8 18.1 + - - +
64D GLY 3.5 7.9 - - - +
66D ALA* 1.3 72.2 - - - +
68D GLY* 1.3 57.9 + - - +
70D ALA* 3.6 6.9 - - - +
71D MET* 3.2 34.9 + - + +
92D GLN* 4.0 19.5 - - - +
96D SER* 3.7 13.0 - - - -
97D ALA* 4.0 31.6 - - + +
110D VAL* 4.2 4.5 - - + +
112D ILE* 3.9 5.1 - - - +
114D PHE* 4.3 13.5 - - + -
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 3.5 20.0 - - - -
148C ILE* 3.3 22.2 - - - +
64D GLY 3.1 10.2 + - - -
65D ILE 3.8 0.7 - - - -
66D ALA 3.0 1.0 - - - -
67D VAL* 1.3 75.8 - - - +
69D ALA* 1.3 65.8 + - - +
70D ALA 3.3 0.7 - - - -
71D MET* 3.2 15.6 + - - +
72D ALA* 3.1 17.3 + - - +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLY 3.7 17.1 - - - +
150C LEU* 4.2 7.9 - - + -
151C ALA* 4.4 4.0 - - - -
24D PHE* 4.0 30.3 - - + -
65D ILE 3.0 16.9 + - - +
66D ALA 3.6 4.7 - - - +
68D GLY* 1.3 73.8 - - - +
70D ALA* 1.3 63.5 + - - +
72D ALA* 2.9 14.4 + - - +
73D GLY 3.1 0.5 + - - -
74D LEU* 3.1 24.0 + - + +
76D PRO* 4.6 0.2 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA 3.0 13.5 + - - +
67D VAL 3.6 11.4 - - - +
69D ALA* 1.3 77.0 - - - +
71D MET* 1.3 60.0 + - - +
73D GLY* 3.2 10.9 + - - -
74D LEU 3.4 11.4 - - - +
76D PRO* 3.7 18.1 - - + +
108D GLN* 4.8 0.2 + - - -
109D PRO 4.0 1.6 - - - +
110D VAL* 4.2 7.9 - - + -
111D PRO* 3.3 41.8 - - - +
112D ILE* 4.3 2.0 - - + +
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Residues in contact with MET 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE* 4.9 1.8 - - + -
127C TYR* 5.7 2.0 - - - -
132C TYR* 3.6 27.9 - - + +
144C LEU* 2.7 48.9 - - + -
148C ILE* 4.6 7.0 - - + -
67D VAL* 3.2 24.1 + - + +
68D GLY* 3.5 9.6 - - - +
69D ALA 3.2 0.8 - - - -
70D ALA* 1.3 76.9 - - - +
72D ALA* 1.3 60.4 + - - +
73D GLY* 3.1 3.3 + - - -
96D SER 5.6 0.7 - - - +
100D THR* 4.8 8.5 - - - -
108D GLN* 2.9 48.1 + - + +
109D PRO 4.5 0.9 - - - -
110D VAL* 4.3 16.6 - - + -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C HIS* 5.7 4.5 - - + +
132C TYR* 4.2 15.8 + - - +
148C ILE* 4.2 14.6 - - + +
151C ALA* 3.3 32.1 - - + -
155C ASN* 5.0 7.9 + - - +
68D GLY 3.1 9.7 + - - +
69D ALA 2.9 4.0 + - - +
71D MET* 1.3 77.1 - - - +
73D GLY* 1.3 58.7 + - - +
74D LEU* 5.6 0.2 - - - -
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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
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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