Contacts of the helix formed by residues 68 - 77 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65K CYS* 3.1 22.4 + - + +
67K GLY* 1.3 78.3 - - - +
69K GLU* 1.3 54.4 + - - -
70K ALA 3.0 6.5 - - - +
71K CYS* 3.0 30.2 + - + +
72K CYS* 3.6 7.6 + - - -
90K ARG* 4.0 16.6 - - - +
94K PHE* 6.0 0.3 - - - -
194K GLU* 3.6 18.3 - - - +
196K ASN* 2.9 33.6 - - - +
227K GLY 5.1 0.2 - - - -
257K THR* 3.3 30.3 - - + +
258K TYR 4.0 3.1 - - - +
259K ARG* 3.4 24.5 - - + +
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Residues in contact with GLU 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K MET* 3.6 34.1 - - + +
42K VAL* 3.6 26.9 - - + +
43K ARG* 2.6 53.8 + - - +
65K CYS* 4.4 1.6 - - - +
66K ASP* 3.1 9.3 - - - +
67K GLY 3.0 16.2 + - - -
68K GLN* 1.3 72.8 - - - +
70K ALA* 1.3 61.6 + - - +
71K CYS 3.0 0.7 + - - -
72K CYS* 4.3 7.9 - - - -
73K VAL* 3.2 28.8 + - + +
287K PRO* 3.3 9.5 - - + +
288K ILE* 4.6 2.0 - - + +
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Residues in contact with ALA 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K MET* 4.2 7.2 - - - -
67K GLY 4.9 0.2 - - - +
68K GLN 3.0 0.2 - - - -
69K GLU* 1.3 80.9 - - - +
71K CYS* 1.3 56.1 + - - +
74K GLY* 3.1 23.6 + - - -
227K GLY 2.9 27.1 - - - +
228K MET 3.7 11.4 - - - +
229K ASP 4.4 0.2 - - - -
230K ILE* 3.8 13.9 - - + +
233K VAL* 3.5 10.5 - - - +
287K PRO* 3.5 26.9 - - + +
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Residues in contact with CYS 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K GLN* 3.0 12.9 + - - +
70K ALA* 1.3 75.5 - - - +
72K CYS* 1.3 61.3 + - - +
74K GLY* 3.0 1.2 + - - -
75K LEU* 2.7 37.4 + - - +
94K PHE* 4.9 2.9 - - + -
194K GLU* 3.7 22.0 - - - +
227K GLY* 3.9 17.5 - - - -
233K VAL* 3.8 6.6 - - - +
255K LEU* 3.6 33.0 - - + -
257K THR* 4.0 20.0 - - - -
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Residues in contact with CYS 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K VAL* 4.7 5.6 - - - -
65K CYS* 4.9 4.0 - - - -
68K GLN 3.6 10.5 + - - -
69K GLU* 4.4 9.0 - - - -
71K CYS* 1.3 79.6 - - - +
73K VAL* 1.3 68.0 + - - +
75K LEU* 4.0 0.7 - - - +
76K GLU* 3.2 16.5 + - - +
93K GLY* 3.7 28.9 - - - -
94K PHE* 3.5 47.7 - - + +
97K THR* 3.4 20.9 + - + -
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Residues in contact with VAL 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K TYR* 4.3 16.8 - - + +
38K MET* 3.7 38.1 - - + +
39K MET* 3.5 23.6 - - + +
42K VAL* 5.1 1.3 - - + -
69K GLU* 3.2 20.6 + - + +
71K CYS 3.2 0.6 - - - -
72K CYS* 1.3 79.5 - - - +
74K GLY* 1.3 66.9 + - - +
75K LEU 3.2 0.9 + - - -
76K GLU* 3.3 11.5 + - - +
77K ALA* 3.3 13.7 + - - +
97K THR* 4.2 13.7 - - + -
230K ILE* 3.6 17.9 - - + +
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Residues in contact with GLY 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ALA 3.1 21.1 + - - -
71K CYS 3.0 3.2 + - - -
73K VAL* 1.3 77.2 - - - +
75K LEU* 1.3 60.9 + - - +
77K ALA* 3.6 6.6 + - - +
78K GLY 3.6 2.9 + - - -
230K ILE* 3.5 19.8 - - - +
233K VAL* 3.7 15.4 - - - +
234K ARG* 3.4 23.7 - - - +
237K THR* 4.3 0.2 + - - -
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Residues in contact with LEU 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K CYS* 2.7 17.4 + - + +
72K CYS* 4.0 4.5 - - - +
74K GLY* 1.3 70.3 - - - +
76K GLU* 1.3 57.0 + - - +
77K ALA 3.0 2.0 - - - -
78K GLY* 2.7 23.9 + - - -
79K ILE* 3.3 14.4 + - - +
85K LEU* 5.0 2.0 - - + -
94K PHE* 3.6 34.1 - - + -
162K LEU* 4.3 20.0 - - + -
164K LEU* 3.9 13.7 - - + -
192K ILE* 4.5 9.9 - - + -
233K VAL* 3.5 20.0 - - + -
237K THR* 3.2 26.7 - - + +
253K MET* 4.1 15.0 - - + -
255K LEU* 4.4 10.5 - - + -
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Residues in contact with GLU 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K MET* 5.5 13.0 - - + -
72K CYS 3.2 16.8 + - - +
73K VAL* 3.3 3.8 + - - +
75K LEU* 1.3 77.2 - - - +
77K ALA* 1.3 57.6 + - - +
78K GLY 3.1 0.2 - - - -
79K ILE* 3.0 31.0 - - - +
80K ASN 4.2 5.9 - - - +
81K PRO* 4.5 5.9 - - - +
85K LEU* 5.3 3.0 - - - +
97K THR* 3.5 34.8 + - - +
98K ARG* 2.9 46.3 + - - -
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Residues in contact with ALA 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K LYS* 6.2 0.9 - - - +
35K TYR* 3.4 40.4 - - + +
38K MET* 6.2 0.9 - - + -
73K VAL 3.3 11.5 + - - +
74K GLY* 3.8 2.2 - - - +
75K LEU 3.0 1.2 + - - -
76K GLU* 1.3 78.4 - - - +
78K GLY* 1.3 58.0 + - - +
79K ILE 3.6 1.8 - - - -
230K ILE* 6.3 0.4 - - + -
234K ARG* 3.4 23.3 - - + +
238K ARG* 3.8 13.5 + - - -
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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