Contacts of the helix formed by residues 68 - 79 (chain A) 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 GLN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A CYS* 3.7 21.5 + - + +
66A ASP 3.2 1.4 - - - -
67A GLY* 1.3 77.9 - - - +
69A GLU* 1.3 57.8 + - - +
70A ALA* 3.3 2.9 - - - -
71A CYS* 2.9 34.6 + - + +
72A CYS* 3.4 7.1 + - - -
90A ARG* 3.8 21.2 - - - +
194A GLU* 3.9 19.4 - - - +
196A ASN* 2.9 45.3 - - - +
227A GLY 5.1 0.2 - - - -
257A THR* 3.5 18.4 - - - +
258A TYR 3.2 13.2 - - - +
259A ARG* 3.6 12.0 - - - +
1003A TPP 5.2 0.4 + - - -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.8 36.4 - - + +
42A VAL* 4.1 19.7 - - + -
43A ARG* 2.5 50.0 + - - +
46A GLU* 6.3 0.2 - - + -
65A CYS 4.1 4.3 - - - +
66A ASP* 3.7 7.3 - - - -
67A GLY* 2.7 33.8 + - - -
68A GLN* 1.3 74.3 - - - +
70A ALA* 1.3 65.8 + - - +
72A CYS* 4.1 7.9 - - - -
73A VAL* 3.1 29.6 + - - +
287A PRO* 3.6 5.3 - - + +
288A ILE* 4.7 2.0 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 3.9 7.0 - - - -
69A GLU* 1.3 72.9 - - - +
71A CYS* 1.3 65.0 + - - +
74A GLY* 2.7 22.7 + - - -
227A GLY 3.0 27.6 - - - +
228A MET* 3.6 24.5 - - - +
229A ASP 3.9 12.8 - - - +
230A ILE* 3.3 12.1 - - - +
233A VAL* 3.7 5.4 - - - +
287A PRO* 4.0 9.3 - - + +
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Residues in contact with CYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN* 2.9 17.8 + - + +
70A ALA* 1.3 81.1 - - - +
72A CYS* 1.3 66.9 + - - +
75A LEU* 2.8 28.7 + - + +
94A PHE* 4.6 1.1 - - + -
194A GLU* 4.3 14.4 - - - +
227A GLY* 3.7 16.8 - - - -
233A VAL* 4.1 9.4 - - - -
255A LEU* 3.7 31.0 - - + -
257A THR* 3.8 25.6 - - - -
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Residues in contact with CYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.3 9.9 - - - -
65A CYS* 5.3 3.4 - - - -
68A GLN 3.4 3.1 + - - +
69A GLU* 3.9 19.1 - - - -
71A CYS* 1.3 78.8 - - - +
73A VAL* 1.3 69.7 + - - +
75A LEU* 4.1 1.1 - - - +
76A GLU* 3.4 15.9 + - - +
93A GLY* 3.6 26.0 - - - +
94A PHE* 3.3 46.5 - - + +
97A THR* 3.6 14.5 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 4.1 30.3 - - + +
38A MET* 3.8 28.0 - - + +
39A MET* 3.7 29.4 - - + +
42A VAL* 5.0 2.2 - - + -
69A GLU* 3.1 17.3 + - + +
71A CYS 2.8 3.6 + - - -
72A CYS* 1.3 77.5 - - - +
74A GLY* 1.3 54.6 + - - +
75A LEU 3.1 1.7 + - - -
76A GLU* 3.2 3.1 + - - +
77A ALA* 2.7 35.3 + - - +
97A THR* 4.3 11.9 - - + -
230A ILE* 4.0 12.6 - - + -
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 2.7 19.9 + - - -
73A VAL* 1.3 71.0 - - - +
75A LEU* 1.3 63.1 + - - +
77A ALA* 3.2 7.8 - - - +
78A GLY 3.2 12.6 + - - -
230A ILE* 3.0 22.9 - - - +
233A VAL* 3.6 16.4 - - - -
234A ARG* 3.5 14.4 - - - -
237A THR* 4.0 1.6 + - - -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A CYS 2.8 16.2 + - - +
72A CYS 4.1 0.2 - - - +
74A GLY* 1.3 72.0 - - - +
76A GLU* 1.3 57.5 + - - +
78A GLY* 2.5 30.0 + - - -
79A ILE* 3.2 12.1 + - - +
85A LEU* 4.7 2.7 - - + -
94A PHE* 3.4 39.9 - - + -
162A LEU* 3.9 23.3 - - + -
164A LEU* 4.3 11.2 - - + -
192A ILE* 4.8 2.9 - - + -
233A VAL* 3.3 23.3 - - + -
237A THR* 3.4 19.0 - - + +
253A MET* 4.3 9.9 - - + -
255A LEU* 4.1 19.7 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 4.4 11.0 - - + -
72A CYS 3.4 15.2 + - - +
73A VAL 3.2 3.9 + - - +
75A LEU* 1.3 76.4 - - - +
77A ALA* 1.3 62.8 + - - +
78A GLY 3.2 1.2 + - - -
79A ILE* 3.4 25.9 + - - +
80A ASN 4.6 0.7 - - - -
81A PRO* 4.6 10.6 - - - +
85A LEU* 4.9 3.2 - - - +
94A PHE* 5.8 0.4 - - - -
97A THR* 3.3 37.6 + - + +
98A ARG* 2.9 46.3 + - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.7 31.5 + - + +
38A MET* 5.7 1.2 - - - +
73A VAL* 2.7 18.6 + - + +
74A GLY* 3.2 17.5 - - - +
75A LEU 2.8 1.8 + - - -
76A GLU* 1.3 72.1 - - - +
78A GLY* 1.3 55.2 + - - -
79A ILE 3.7 2.5 - - - +
230A ILE* 5.3 0.7 - - + -
234A ARG* 3.5 24.8 - - + +
238A ARG* 4.4 6.4 + - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLY 3.2 6.4 + - - -
75A LEU 2.5 17.9 + - - -
77A ALA* 1.3 73.2 - - - +
79A ILE* 1.3 60.4 + - - +
234A ARG* 4.3 3.4 - - - -
237A THR* 3.8 17.9 - - - +
238A ARG* 3.8 33.7 + - - +
241A ALA* 4.3 6.4 - - - +
245A ARG* 5.1 0.9 + - - -
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.2 11.2 + - - +
76A GLU* 3.4 29.4 + - - +
77A ALA 4.5 2.1 - - - +
78A GLY* 1.3 83.3 - - - +
80A ASN* 1.3 74.6 + - - +
81A PRO* 4.6 0.9 - - - +
83A ASP* 3.5 18.4 - - + +
84A HIS 5.1 0.9 - - - +
85A LEU* 4.0 21.3 - - + -
98A ARG* 3.3 31.4 - - - +
160A VAL* 4.6 3.8 - - + -
162A LEU* 3.6 38.6 - - + -
237A THR* 3.9 7.4 - - + -
241A ALA* 5.1 3.6 - - + -
245A ARG* 4.8 2.2 - - - +
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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