Contacts of the helix formed by residues 57 - 68 (chain A) in PDB entry 3EVA
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 ARG 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.2 20.6 + - - +
35A VAL* 3.0 45.9 + - + +
37A ARG* 3.6 30.0 - - + +
41A ARG* 3.7 25.0 - - - +
56A SER* 1.3 73.5 - - - +
58A GLY* 1.3 62.2 + - - +
59A THR 3.3 0.8 + - - -
60A ALA* 3.4 14.8 + - - +
61A LYS* 3.5 13.6 + - + +
211A LEU* 5.4 0.5 - - - +
213A ARG* 3.4 31.8 - - - +
256A ASP* 5.7 0.2 - - - -
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Residues in contact with GLY 58 (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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56A SER* 3.0 6.0 + - - -
57A ARG* 1.3 77.8 - - - +
59A THR* 1.3 64.8 + - - +
61A LYS* 3.1 11.0 + - - +
62A LEU 3.0 11.6 + - - -
87A TRP* 3.0 28.4 + - - -
146A ASP* 5.4 1.1 - - - -
901A SAH 3.2 20.6 - - - -
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Residues in contact with THR 59 (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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54A ALA* 3.5 29.3 - - + +
55A VAL 4.5 0.5 + - - -
56A SER* 3.5 2.5 + - - -
57A ARG 3.3 0.6 - - - -
58A GLY* 1.3 75.9 - - - +
60A ALA* 1.3 59.2 + - - +
62A LEU* 3.4 2.8 + - - +
63A ARG* 2.9 26.7 + - - +
86A GLY* 2.8 30.3 + - - -
87A TRP* 4.7 0.9 - - - -
89A TYR* 5.3 2.3 - - - +
90A TYR* 3.9 24.4 + - + -
257A VAL* 3.8 30.1 - - + -
259A LEU* 4.7 6.9 - - + +
901A SAH 4.0 2.2 + - - -
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Residues in contact with ALA 60 (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 VAL* 3.6 33.9 - - + -
56A SER 4.8 0.2 + - - -
57A ARG 3.4 9.9 + - - +
58A GLY 3.2 0.4 - - - -
59A THR* 1.3 79.4 - - - +
61A LYS* 1.3 62.0 + - - +
63A ARG* 3.4 8.2 + - - +
64A TRP* 3.1 18.7 + - - +
211A LEU* 3.5 16.2 - - + +
256A ASP* 4.2 6.7 + - - +
257A VAL* 3.8 20.3 - - + +
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Residues in contact with LYS 61 (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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57A ARG 3.5 7.0 + - - +
58A GLY* 3.1 18.7 + - - +
60A ALA* 1.3 79.4 - - - +
62A LEU* 1.3 61.6 + - - +
64A TRP* 3.3 8.3 + - - +
65A PHE* 3.5 6.9 + - + -
87A TRP* 4.4 6.1 - - + +
146A ASP* 5.0 6.5 + - - +
182A LYS* 5.7 0.6 - - - +
209A ASN* 3.0 35.4 + - - +
211A LEU* 3.8 18.3 - - + +
212A SER* 3.6 21.5 - - - +
218A GLU* 2.6 32.5 + - - -
220A TYR* 3.1 27.1 + - + +
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Residues in contact with LEU 62 (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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58A GLY 3.0 7.7 + - - +
59A THR 3.9 3.1 - - - +
61A LYS* 1.3 73.8 - - - +
63A ARG* 1.3 66.1 + - - +
65A PHE* 3.1 6.3 + - + -
66A HIS* 2.9 21.2 + - - +
71A VAL* 4.1 22.7 - - + -
73A LEU* 4.3 9.9 - - + -
87A TRP* 3.7 61.2 - - + +
90A TYR* 3.9 20.6 - - + -
144A LEU* 4.0 19.7 - - + -
180A CYS* 4.3 17.9 - - - -
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Residues in contact with ARG 63 (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 VAL* 4.7 3.2 - - - +
59A THR 2.9 18.0 + - - +
60A ALA* 3.6 15.0 + - - +
62A LEU* 1.3 77.6 - - - +
64A TRP* 1.3 56.2 + - - +
67A GLU* 2.8 56.2 + - + +
90A TYR* 3.6 35.8 - - + +
254A GLU* 5.2 6.9 - - - +
255A ALA 3.6 19.8 + - - -
256A ASP 4.4 2.8 + - - -
257A VAL* 3.2 41.6 - - + +
258A ILE 5.3 0.2 - - - +
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Residues in contact with TRP 64 (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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60A ALA 3.1 13.3 + - - +
61A LYS 3.5 9.4 - - - +
62A LEU 3.2 0.4 - - - -
63A ARG* 1.3 79.0 - - - +
65A PHE* 1.3 99.1 + + - +
67A GLU* 3.4 13.7 - - - +
68A ARG* 2.8 71.6 + - - +
70A TYR* 3.8 18.6 - + - -
207A ILE* 3.9 4.0 - - + -
208A ARG 3.8 12.3 - - - -
209A ASN* 3.7 14.1 - - - +
210A PRO* 3.3 40.6 - - + +
211A LEU* 4.6 6.1 - - + -
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Residues in contact with PHE 65 (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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61A LYS* 3.5 15.9 + - + -
62A LEU* 3.1 11.4 + - + +
64A TRP* 1.3 107.4 - + - +
66A HIS* 1.3 62.4 + - - +
68A ARG* 3.5 1.0 + - - +
69A GLY 3.4 3.3 + - - -
70A TYR* 2.9 46.9 + - + +
71A VAL* 3.9 16.2 - - + -
87A TRP* 5.3 2.0 - + - -
180A CYS* 3.7 16.6 - - - -
207A ILE* 4.0 20.9 - - + -
209A ASN* 3.3 23.3 - - + -
220A TYR* 3.5 52.0 - + + -
222A VAL* 4.5 3.1 - - + -
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Residues in contact with HIS 66 (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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62A LEU 2.9 15.6 + - - +
63A ARG 3.7 2.7 - - - +
65A PHE* 1.3 78.4 - - - +
67A GLU* 1.3 62.6 + - - +
68A ARG 3.1 1.4 + - - -
69A GLY* 3.2 11.6 + - - -
71A VAL* 3.5 25.0 - - + +
72A LYS* 4.6 1.3 - - - -
73A LEU* 3.7 32.2 + - + +
90A TYR* 2.7 30.8 + + + -
94A GLN* 3.3 33.7 - - + +
96A GLU* 5.2 5.0 + - - -
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Residues in contact with GLU 67 (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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63A ARG* 2.8 49.0 + - + +
64A TRP* 3.4 23.6 - - - +
66A HIS* 1.3 74.8 + - - +
68A ARG* 1.3 83.8 + - - +
69A GLY 3.5 0.7 - - - -
90A TYR* 5.3 1.1 - - - +
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Residues in contact with ARG 68 (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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64A TRP* 2.8 63.7 + - - +
65A PHE 3.7 1.1 - - - +
66A HIS 3.1 0.2 - - - -
67A GLU* 1.3 104.7 + - - +
69A GLY* 1.3 61.9 + - - +
70A TYR* 3.4 34.3 + - + -
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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