Contacts of the helix formed by residues 68 - 77 (chain U) in PDB entry 3EXG
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 GLN 68 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65U CYS* 3.0 23.6 + - + +
67U GLY* 1.3 82.7 - - - +
69U GLU* 1.3 56.8 + - - +
70U ALA* 3.1 3.6 - - - -
71U CYS* 2.9 34.6 + - + +
72U CYS* 4.0 3.1 + - - -
90U ARG* 4.0 13.6 - - - +
94U PHE* 5.9 0.2 - - - -
194U GLU* 3.5 24.7 + - - +
196U ASN* 2.9 34.4 - - - +
227U GLY 5.3 0.7 - - - -
257U THR* 3.4 30.3 - - + +
258U TYR 4.2 4.5 - - - +
259U ARG* 3.5 22.4 - - + +
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Residues in contact with GLU 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U MET* 3.9 27.1 - - + +
42U VAL* 3.1 32.5 - - + +
43U ARG* 2.5 59.5 + - - -
65U CYS 4.5 2.0 - - - +
66U ASP* 3.4 10.6 - - - -
67U GLY 3.2 11.6 + - - -
68U GLN* 1.3 72.1 + - - +
70U ALA* 1.3 61.5 + - - +
71U CYS 2.9 1.8 + - - -
72U CYS* 4.1 8.1 - - - -
73U VAL* 3.1 27.8 + - + +
287U PRO* 3.6 7.2 - - + +
288U ILE* 4.5 1.8 - - - -
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Residues in contact with ALA 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39U MET* 4.2 8.9 - - - -
68U GLN 3.0 1.0 + - - -
69U GLU* 1.3 77.5 - - - +
71U CYS* 1.3 56.4 + - - +
74U GLY* 2.9 25.6 + - - +
227U GLY 2.9 24.5 - - - +
228U MET 3.7 1.6 - - - -
229U ASP 4.1 0.2 - - - -
230U ILE* 3.5 29.8 - - + +
233U VAL* 3.3 9.5 - - - +
287U PRO* 3.7 23.9 - - + +
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Residues in contact with CYS 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U GLN* 2.9 21.8 + - + +
70U ALA* 1.3 77.3 - - - +
72U CYS* 1.3 64.2 + - - +
75U LEU* 2.8 35.6 + - - +
94U PHE* 4.8 9.6 - - + -
194U GLU* 5.4 7.6 - - + +
227U GLY* 3.8 24.2 - - - -
233U VAL* 4.3 5.4 - - - -
255U LEU* 3.7 31.2 - - + -
257U THR* 4.5 12.8 - - - -
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Residues in contact with CYS 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U VAL* 4.7 6.3 - - - -
65U CYS* 5.0 5.2 - - - -
68U GLN 4.7 1.8 - - - -
69U GLU* 3.9 18.6 - - - -
71U CYS* 1.3 81.4 - - - +
73U VAL* 1.3 67.2 + - - +
75U LEU* 4.1 0.3 - - - +
76U GLU* 3.1 25.3 + - - +
93U GLY* 4.1 17.5 - - - -
94U PHE* 3.5 42.6 - - + +
97U THR* 3.8 25.1 + - + +
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Residues in contact with VAL 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U TYR* 4.1 13.5 - - + +
38U MET* 4.0 27.6 - - + +
39U MET* 3.7 35.2 - - + +
42U VAL* 5.0 1.6 - - + -
69U GLU* 3.1 18.7 + - + +
72U CYS* 1.3 81.6 - - - +
74U GLY* 1.3 63.1 + - - +
76U GLU* 3.6 3.8 + - - +
77U ALA* 3.2 19.8 + - - +
97U THR* 4.1 16.2 - - + -
230U ILE* 3.9 19.5 - - + -
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Residues in contact with GLY 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U ALA 2.9 14.0 + - - -
73U VAL* 1.3 78.9 - - - +
75U LEU* 1.3 62.0 + - - +
77U ALA* 3.1 18.2 + - - +
78U GLY* 3.4 4.2 + - - -
230U ILE* 4.0 16.9 - - - +
233U VAL* 3.0 25.6 - - - -
234U ARG* 3.5 11.9 - - - -
237U THR* 4.6 0.2 - - - -
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Residues in contact with LEU 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71U CYS 2.8 20.3 + - - +
72U CYS* 4.1 3.1 - - - +
74U GLY* 1.3 74.8 - - - +
76U GLU* 1.3 60.0 + - - +
78U GLY* 2.8 21.1 + - - -
79U ILE* 3.4 12.0 + - - +
85U LEU* 4.4 2.2 - - + -
94U PHE* 3.8 29.6 - - + -
162U LEU* 3.7 28.0 - - + -
164U LEU* 4.2 7.6 - - + -
192U ILE* 4.1 12.8 - - + -
233U VAL* 3.6 9.0 - - + -
237U THR* 3.4 25.9 - - - +
253U MET* 4.1 4.7 - - + -
255U LEU* 3.6 26.7 - - + -
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Residues in contact with GLU 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U MET* 5.5 10.5 - - + -
72U CYS 3.1 16.8 + - - +
73U VAL* 4.0 4.3 - - - +
75U LEU* 1.3 79.3 - - - +
77U ALA* 1.3 56.0 + - - +
78U GLY 3.1 4.2 + - - -
79U ILE* 3.2 28.3 - - - +
81U PRO* 4.8 7.3 - - - +
85U LEU* 5.7 2.9 - - - +
94U PHE* 5.9 1.2 - - - -
97U THR* 3.1 37.1 + - - +
98U ARG* 3.2 48.2 + - - +
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Residues in contact with ALA 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U LYS* 5.7 3.4 - - - +
35U TYR* 3.5 39.3 + - + +
73U VAL 3.2 14.1 + - - +
74U GLY* 3.1 13.2 + - - +
75U LEU 3.1 1.4 + - - -
76U GLU* 1.3 76.6 - - - +
78U GLY* 1.3 56.5 + - - +
79U ILE 3.6 0.9 - - - -
230U ILE* 5.6 0.2 - - + -
234U ARG* 3.6 12.0 - - + +
238U ARG* 2.9 23.9 + - - -
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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