Contacts of the helix formed by residues 55 - 70 (chain A) in PDB entry 5E2Q
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 GLU 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A SER* 3.3 13.8 + - - -
54A PRO* 1.3 87.4 - - - +
56A ALA* 1.3 65.2 + - - +
57A PRO* 3.4 1.8 - - - -
58A TYR* 3.2 12.8 + - + +
59A ILE* 3.0 32.5 + - + +
105A ASN* 2.7 31.3 + - - +
106A TYR* 4.0 4.9 + - - -
113A LYS* 4.0 11.8 + - - -
146A THR 5.5 0.2 - - - +
147A CYS* 4.3 13.7 - - + -
150A LEU* 3.4 47.2 - - + +
168A ILE* 5.8 0.3 - - - +
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Residues in contact with ALA 56 (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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49A LEU* 3.3 29.4 - - + +
53A SER* 3.1 21.1 + - - +
55A GLU* 1.3 77.7 - - - +
57A PRO* 1.4 65.4 - - + +
59A ILE* 3.4 7.1 + - - +
60A TYR* 3.1 23.7 + - - +
99A VAL* 5.3 1.3 - - - +
104A GLY* 4.0 20.2 - - - -
105A ASN* 4.0 10.1 - - - +
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.6 22.6 - - + +
50A LEU* 3.6 30.3 - - + -
53A SER 3.4 14.1 - - - +
54A PRO 3.7 6.5 - - - +
55A GLU 3.6 3.1 - - - -
56A ALA* 1.4 91.9 - - + +
58A TYR* 1.3 61.3 + - - +
60A TYR* 3.5 2.8 + - - +
61A ALA* 3.1 22.7 + - - +
715A LEU* 3.6 34.7 - - + +
719A ALA* 3.8 10.8 - - + -
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Residues in contact with TYR 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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54A PRO 3.6 24.0 - - - -
55A GLU* 3.2 12.9 + - + +
57A PRO* 1.3 75.2 - - - +
59A ILE* 1.3 57.6 + - - +
61A ALA* 3.0 5.9 + - - +
62A LEU* 2.8 29.3 + - - +
143A LEU* 3.8 27.0 - - + +
146A THR* 3.6 34.5 - - + +
147A CYS* 3.6 19.5 - - + -
716A THR* 4.2 11.9 - - + -
719A ALA* 3.4 19.6 + - + -
720A THR* 3.2 45.5 + - + +
723A ALA* 4.7 6.6 - - + +
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Residues in contact with ILE 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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55A GLU* 3.0 34.2 + - + +
56A ALA* 3.8 5.8 - - - +
57A PRO 3.3 0.2 - - - -
58A TYR* 1.3 76.3 - - - +
60A TYR* 1.3 57.1 + - - +
62A LEU* 3.2 4.3 + - - +
63A LEU* 2.9 54.1 + - + +
95A TYR* 3.3 30.7 - - + +
99A VAL* 4.2 11.4 - - + -
105A ASN* 4.3 14.6 - - + +
147A CYS* 4.0 21.8 - - + -
151A MET* 4.2 21.3 - - + -
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Residues in contact with TYR 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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46A LEU* 3.6 16.2 - - + +
49A LEU* 3.6 28.3 - - + -
56A ALA 3.1 12.4 + - - +
57A PRO 3.8 1.8 - - - +
59A ILE* 1.3 77.1 - - - +
61A ALA* 1.3 60.3 + - - +
63A LEU* 4.0 4.4 - - - +
64A SER* 2.9 43.5 + - - -
99A VAL* 4.8 6.7 - - + +
100A TYR* 3.5 35.9 - + - -
103A MET* 4.1 12.1 - - + -
700A PHE* 4.6 9.1 + + + +
704A PHE* 3.3 33.3 - - - -
711A LEU* 5.4 3.5 - - + +
712A GLU* 5.1 5.8 - - + -
715A LEU* 3.5 30.7 - - + -
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Residues in contact with ALA 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 PRO 3.1 13.4 + - - +
58A TYR 3.0 9.7 + - - +
60A TYR* 1.3 83.8 - - + +
62A LEU* 1.3 57.3 + - - +
64A SER* 3.9 1.4 - - - -
65A ARG* 3.1 33.9 + - - +
143A LEU* 3.8 12.8 - - + -
712A GLU* 4.0 22.4 - - + +
715A LEU* 5.5 0.4 - - + -
716A THR* 3.7 22.4 - - - +
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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 TYR 2.8 15.0 + - - +
59A ILE* 3.7 5.6 - - - +
61A ALA* 1.3 74.5 - - - +
63A LEU* 1.3 62.5 + - + +
65A ARG* 3.4 4.1 + - + +
66A LEU* 3.0 45.0 + - + +
127A ILE* 3.9 41.5 - - + -
140A VAL* 4.3 17.0 - - + +
143A LEU* 3.6 23.9 - - + +
144A TRP* 3.9 21.1 - - + +
147A CYS* 4.1 16.4 - - - -
151A MET* 4.3 8.7 - - + -
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Residues in contact with LEU 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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59A ILE* 2.9 37.9 + - + +
60A TYR* 4.0 3.1 - - - +
62A LEU* 1.3 79.7 - - + +
64A SER* 1.3 62.5 + - - +
66A LEU* 3.3 6.9 + - + +
67A PHE* 3.0 35.8 + - + +
92A PHE* 3.8 35.4 - - + -
95A TYR* 4.9 4.5 - - + -
96A ALA* 3.7 31.9 - - + +
99A VAL* 4.0 17.7 - - + -
100A TYR* 3.5 17.7 - - + +
127A ILE* 6.4 0.4 - - + -
151A MET* 5.7 4.5 - - + -
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Residues in contact with SER 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 TYR* 2.9 35.0 + - - -
61A ALA 3.9 0.9 - - - -
63A LEU* 1.3 76.4 - - - +
65A ARG* 1.3 61.0 + - - +
67A PHE* 4.1 1.6 - - - +
68A ARG* 3.0 38.8 + - - +
100A TYR* 3.5 11.2 + - - -
708A GLY 5.0 0.3 + - - -
712A GLU* 2.4 35.1 + - - +
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Residues in contact with ARG 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 ALA* 3.1 19.5 + - - +
62A LEU* 3.6 5.6 - - + +
64A SER* 1.3 74.8 - - - +
66A LEU* 1.3 65.9 + - + +
68A ARG* 3.4 12.6 + - - +
69A ALA* 3.4 7.4 + - - +
132A ALA* 3.4 22.7 + - + +
136A HIS* 3.7 27.9 + - - +
139A GLU* 3.5 41.2 + - - +
140A VAL* 4.4 16.6 - - + -
143A LEU* 4.1 18.3 - - - +
709A PRO* 5.6 3.2 + - - +
712A GLU* 3.2 33.5 + - - +
713A GLU* 4.5 14.3 + - - +
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Residues in contact with LEU 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* 3.0 32.3 + - + +
63A LEU* 3.3 8.7 + - + +
65A ARG* 1.3 78.3 - - + +
67A PHE* 1.3 62.8 + - + +
69A ALA* 3.6 3.1 + - - +
70A GLN* 3.1 29.7 + - - +
75A LEU* 4.8 14.4 - - + +
92A PHE* 4.0 23.8 - - + -
126A VAL* 6.0 1.1 - - + -
127A ILE* 3.9 37.7 - - + -
130A SER* 3.2 36.1 - - - +
132A ALA* 4.0 8.4 + - + +
140A VAL* 5.5 1.3 - - + -
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Residues in contact with PHE 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 LEU* 3.0 31.6 + - + +
64A SER* 4.6 1.3 - - - +
66A LEU* 1.3 77.4 - - + +
68A ARG* 1.3 62.8 + - - +
69A ALA 3.4 0.2 - - - -
70A GLN 3.2 28.6 - - - +
71A ASP* 3.9 5.8 + - - +
72A PRO* 4.0 15.7 - - + -
75A LEU* 3.7 17.9 - - + -
92A PHE* 3.7 29.8 - + - -
93A LEU* 4.1 11.2 - - + -
96A ALA* 3.9 21.1 - - + -
100A TYR* 4.1 7.9 - - - +
697A ILE* 3.6 40.4 - - + -
701A SER* 3.8 25.8 + - - +
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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 SER* 3.0 38.9 + - - +
65A ARG* 3.8 5.6 - - - +
66A LEU 3.3 0.2 - - - -
67A PHE* 1.3 78.1 - - - +
69A ALA* 1.3 62.1 + - + +
700A PHE 5.6 2.4 + - - -
701A SER* 4.6 18.9 + - - +
704A PHE* 4.1 10.3 + - - +
708A GLY* 3.3 24.7 - - - -
709A PRO* 3.8 27.0 - - - +
712A GLU* 2.3 36.3 + - - -
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Residues in contact with ALA 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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65A ARG 3.4 8.4 + - - +
66A LEU 4.1 1.3 - - - +
67A PHE 3.4 0.2 - - - -
68A ARG* 1.3 82.8 - - - +
70A GLN* 1.3 63.9 + - - +
74A GLN* 4.0 7.4 + - - +
131A GLU* 4.0 17.7 - - + +
132A ALA* 3.7 33.9 - - + +
135A GLN* 4.4 12.5 + - - +
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Residues in contact with GLN 70 (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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66A LEU 3.1 10.0 + - - +
67A PHE* 3.2 27.1 - - - -
68A ARG 3.4 0.2 - - - -
69A ALA* 1.3 84.5 - - - +
71A ASP* 1.3 64.8 + - - +
74A GLN* 3.3 32.4 + - + +
75A LEU* 3.6 30.0 - - + +
78A HIS* 4.2 14.2 - - - +
130A SER* 3.9 3.5 - - - -
131A GLU* 3.1 41.8 + - + +
132A ALA 4.7 0.5 + - - -
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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