Contacts of the helix formed by residues 62 - 81 (chain A) in PDB entry 2YEV
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 THR 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ASN 3.7 17.0 - - - +
59A GLN* 3.3 36.5 + - - +
61A LEU* 1.3 81.3 - - - +
63A GLY* 1.3 69.2 + - - +
64A GLU 3.3 0.3 + - - -
65A GLN* 3.1 25.5 + - - +
66A TYR* 3.2 4.1 + - - -
450A TYR* 3.6 20.4 - - + -
299B PRO* 5.1 6.4 - - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 1.3 72.8 - - - +
64A GLU* 1.3 64.2 + - - -
66A TYR* 3.1 3.8 + - - +
67A ASN* 3.0 24.8 + - - +
450A TYR* 3.4 18.9 - - - +
203B ALA* 3.5 26.2 - - - -
299B PRO* 4.1 13.7 - - - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR 3.3 0.6 + - - -
63A GLY* 1.3 70.5 - - - -
65A GLN* 1.3 72.6 + - - +
67A ASN* 3.2 6.8 + - - +
68A GLN* 2.8 42.9 + - - +
132A GLY 4.9 0.9 - - - +
136A SER* 2.8 30.4 + - - -
149A SER* 4.8 1.0 + - - -
151A SER* 3.7 14.7 + - - -
202B GLY* 5.2 0.7 - - - -
203B ALA* 3.7 27.3 + - + +
299B PRO* 5.0 1.4 - - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.9 16.8 - - + -
62A THR* 3.1 16.8 + - - +
63A GLY* 5.1 0.2 - - - -
64A GLU* 1.3 93.7 + - - +
66A TYR* 1.3 63.7 + - - +
68A GLN* 3.2 19.8 + - - +
69A ILE* 3.1 26.9 + - - +
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Residues in contact with TYR 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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49A ILE* 3.4 40.7 - - + +
52A GLN* 3.9 14.1 - - + -
53A LEU* 3.6 15.0 - - + +
61A LEU* 3.7 41.6 - - + +
62A THR 3.2 5.7 + - - -
63A GLY 3.1 8.8 + - - +
65A GLN* 1.3 76.7 - - - +
67A ASN* 1.3 68.3 + - - +
69A ILE* 3.1 3.6 + - - +
70A LEU* 2.8 51.6 + - + +
380A TYR* 4.4 4.2 + - - -
448A ARG* 4.6 3.0 + - - -
449A TYR 3.8 7.4 + - - -
450A TYR* 3.3 43.1 - - + -
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Residues in contact with ASN 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 GLY* 3.0 10.6 + - - +
64A GLU* 3.2 8.9 + - - +
66A TYR* 1.3 88.2 - - - +
68A GLN* 1.3 54.8 + - - +
70A LEU* 3.7 9.5 - - - +
71A THR* 2.7 36.9 + - - -
136A SER* 3.6 23.4 + - - +
448A ARG 4.3 6.4 - - - +
450A TYR* 4.9 4.0 + - - +
200B LEU* 3.7 21.6 - - + +
202B GLY* 3.1 33.9 + - - -
203B ALA* 3.8 10.3 + - - +
205B HIS* 5.3 0.4 - - - +
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Residues in contact with GLN 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 GLU* 2.8 31.3 + - - +
65A GLN* 3.4 26.3 + - - +
66A TYR 3.1 0.2 - - - -
67A ASN* 1.3 75.5 - - - +
69A ILE* 1.3 67.5 + - + +
71A THR* 3.2 2.8 + - - -
72A LEU* 2.9 29.7 + - + +
132A GLY 3.1 19.2 + - - -
133A GLY* 3.8 3.0 - - - -
134A ALA* 2.9 45.7 + - + +
135A PRO 3.5 9.1 - - - +
136A SER* 3.7 6.7 - - - -
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Residues in contact with ILE 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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45A PHE* 3.6 54.8 - - + +
48A LEU* 4.5 11.4 - - + -
49A ILE* 3.9 10.3 - - + -
61A LEU* 3.9 26.2 - - + -
65A GLN 3.1 14.5 + - - +
66A TYR 3.7 5.6 - - - +
68A GLN* 1.3 77.0 - - + +
70A LEU* 1.3 52.9 + - - +
72A LEU* 3.3 11.5 + - + +
73A HIS* 2.7 32.9 + - - +
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Residues in contact with LEU 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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49A ILE* 3.9 22.5 - - + +
66A TYR* 2.8 40.1 + - + +
67A ASN* 3.7 11.9 - - - +
69A ILE* 1.3 72.6 - - - +
71A THR* 1.3 63.0 + - - +
73A HIS* 3.1 10.0 + - + +
74A GLY* 3.1 20.1 + - - -
138A GLY* 5.8 3.4 - - - -
448A ARG* 3.5 48.0 - - + +
200B LEU* 5.3 5.2 - - + -
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Residues in contact with THR 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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67A ASN 2.7 23.5 + - - -
68A GLN 3.2 0.4 + - - -
70A LEU* 1.3 76.7 - - - +
72A LEU* 1.3 63.5 + - + +
74A GLY* 3.4 0.6 + - - -
75A ALA* 3.0 24.1 + - + +
135A PRO* 3.5 36.3 - - + +
136A SER 3.5 4.9 - - - -
138A GLY* 2.9 49.6 + - - +
139A TRP* 4.0 7.1 - - - +
156A TYR* 4.7 8.1 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.7 30.3 - - + -
68A GLN* 2.9 20.3 + - + +
69A ILE* 3.7 9.9 - - + +
71A THR* 1.3 73.2 - - + +
73A HIS* 1.3 65.5 + - - +
75A ALA* 4.9 4.0 - - + -
76A THR* 2.8 33.6 + - - +
124A ALA* 4.6 13.5 - - + +
125A LEU* 4.3 23.6 - - + +
127A SER* 5.7 0.2 - - - +
128A TYR* 6.4 1.3 - - + -
134A ALA* 3.7 29.6 - - + -
135A PRO* 4.5 14.6 - - + +
156A TYR* 6.5 0.2 - - + -
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Residues in contact with HIS 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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42A ALA* 2.9 28.7 + - - +
45A PHE* 4.0 15.0 - - + -
46A SER* 3.5 21.2 + - - -
49A ILE* 4.0 22.7 - - + -
69A ILE 2.7 17.8 + - - +
70A LEU* 3.4 14.1 - - + +
72A LEU* 1.3 75.7 - - - +
74A GLY* 1.3 68.4 + - - +
77A MET* 3.1 48.4 + - + +
387A HIS* 4.1 23.5 + + - -
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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 LEU* 3.1 10.2 + - - -
71A THR 4.0 1.3 - - - -
73A HIS* 1.3 85.4 - - - +
75A ALA* 1.3 59.9 + - - +
77A MET* 3.5 4.2 + - - +
78A LEU* 3.0 38.0 + - - +
139A TRP* 4.4 14.4 - - - -
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Residues in contact with ALA 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 THR* 3.0 18.2 + - + +
72A LEU* 4.5 4.3 - - + +
74A GLY* 1.3 72.6 - - - +
76A THR* 1.3 61.5 + - - +
78A LEU* 4.8 1.3 - - - -
79A PHE* 2.8 43.9 + - + +
80A PHE* 4.5 5.1 - - + -
139A TRP* 4.0 7.6 - - + +
156A TYR* 3.6 39.3 - - + +
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Residues in contact with THR 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 ALA* 3.6 37.2 - - + +
41A LEU* 4.9 9.1 - - + +
42A ALA* 3.7 12.3 - - + +
45A PHE* 4.7 3.3 - - - -
72A LEU* 2.8 28.8 + - - +
75A ALA* 1.3 76.8 - - - +
77A MET* 1.3 58.7 + - - +
80A PHE* 2.9 49.4 + - + +
81A PHE* 3.2 7.6 + - - +
125A LEU* 4.6 12.9 - - + +
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Residues in contact with MET 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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39A PHE* 3.5 54.5 - - + +
42A ALA* 3.6 11.7 - - + -
43A GLY* 3.6 19.3 - - - +
73A HIS* 3.1 39.2 + - + +
74A GLY* 3.8 4.3 - - - +
76A THR* 1.3 80.5 - - - +
78A LEU* 1.3 63.0 + - + +
81A PHE* 3.4 12.8 - - + +
82A ILE* 3.0 33.2 + - - +
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Residues in contact with LEU 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* 3.0 19.7 + - - +
75A ALA* 4.2 2.0 - - - +
77A MET* 1.3 84.9 - - + +
79A PHE* 1.3 67.0 + - + +
82A ILE* 4.2 2.2 - - + -
83A ILE* 3.2 27.7 + - - +
139A TRP* 3.5 53.6 - - + +
252A THR* 6.0 0.7 - - + -
253A VAL* 6.0 2.5 - - + -
256A MET* 3.6 31.8 - - + +
390A LEU* 3.8 30.5 - - + -
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Residues in contact with PHE 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 ALA* 2.8 35.6 + - + +
78A LEU* 1.3 78.9 - - + +
80A PHE* 1.3 73.7 + + + +
83A ILE* 3.8 8.4 - - + +
84A GLN* 2.9 26.6 + - - -
139A TRP* 4.1 27.4 - + - -
156A TYR* 3.5 25.6 - + - -
160A ILE* 4.2 19.1 - - + -
163A LEU* 3.7 27.3 - - + +
212A LEU* 3.8 31.9 - - + -
245A PHE* 5.9 0.7 - + - -
248A TYR* 4.8 11.0 - + - -
252A THR* 5.4 4.0 - - + -
256A MET* 5.9 1.3 - - + -
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Residues in contact with PHE 80 (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 ALA* 3.3 21.1 - - - -
38A ALA* 3.5 15.2 - - + +
75A ALA* 4.5 4.9 - - + -
76A THR* 2.9 40.0 + - + +
79A PHE* 1.3 97.7 - + + +
81A PHE* 1.3 58.5 + - - +
84A GLN* 3.6 5.7 - - - +
117A PHE* 3.5 18.9 - + - -
120A ALA* 3.9 15.3 - - + -
121A ILE* 3.6 57.0 - - + -
124A ALA* 4.0 19.5 - - + -
125A LEU* 5.6 2.7 - - + -
156A TYR* 6.5 0.9 - + - -
159A ALA* 5.0 4.0 - - + -
163A LEU* 4.2 11.7 - - + -
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Residues in contact with PHE 81 (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 ALA* 3.3 24.7 - - - +
36A PHE* 3.8 25.4 - + - -
38A ALA* 4.2 0.2 - - + -
39A PHE* 3.3 50.0 - + + +
76A THR 3.2 7.5 + - - +
77A MET* 3.4 22.1 + - - +
79A PHE 3.7 0.2 - - - -
80A PHE* 1.3 79.6 - - - +
82A ILE* 1.3 98.0 + - + +
83A ILE 3.2 1.8 - - - -
84A GLN* 2.9 13.7 + - - +
85A ALA* 3.0 27.3 + - + +
390A LEU 5.8 0.4 - - - -
395A GLY* 4.9 6.7 - - - -
398A ALA* 4.2 11.2 - - + -
399A PHE* 5.0 3.6 - + - -
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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
------------------------------------------------------------
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