Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 3W31
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 ASN 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASN* 3.4 19.2 + - - +
58A GLY 4.5 0.5 + - - -
59A ASP* 3.5 16.8 + - - +
60A GLY* 1.3 75.3 + - - +
62A ALA* 1.3 63.9 + - - +
63A SER 3.4 2.2 - - - -
64A GLY 3.2 2.0 + - - -
65A CYS* 2.9 48.0 + - - -
81A ALA* 4.5 2.6 + - - +
82A PRO 3.1 28.3 + - - +
83A VAL* 4.8 3.0 - - - +
84A PRO* 4.0 19.0 - - + +
87A ILE* 3.8 14.8 - - + -
162A GLN* 3.3 11.8 - - - +
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Residues in contact with ALA 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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60A GLY* 2.7 12.5 + - - +
61A ASN* 1.3 71.6 - - - +
63A SER* 1.3 64.5 + - - +
65A CYS* 2.9 16.2 + - - +
66A ALA* 3.0 14.2 + - - +
145A HIS* 3.4 32.3 - - + +
146A TRP* 4.0 16.0 - - + +
162A GLN* 2.9 20.6 + - - +
170A TYR* 5.5 0.9 - - - +
100B GLN* 4.5 9.2 - - - +
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Residues in contact with SER 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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60A GLY 4.1 2.2 + - - -
62A ALA* 1.3 76.2 - - - +
64A GLY* 1.3 61.8 + - - -
66A ALA 3.5 0.5 + - - -
67A LEU* 3.2 22.3 + - - +
87A ILE* 3.9 11.6 - - - +
91A MET* 3.7 19.4 - - - +
137A MET* 3.7 5.3 - - - +
146A TRP* 3.7 37.1 - - - -
98B ALA* 3.5 32.6 + - - +
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Residues in contact with GLY 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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61A ASN 3.2 6.2 + - - -
62A ALA 3.1 1.0 - - - -
63A SER* 1.3 78.7 + - - +
65A CYS* 1.3 65.6 + - - +
67A LEU* 3.2 2.4 + - - +
68A HIS* 3.1 28.8 + - - +
81A ALA* 4.1 6.1 - - - -
82A PRO* 4.1 14.6 - - - -
87A ILE* 4.0 8.7 - - - +
91A MET* 4.1 16.6 - - - -
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Residues in contact with CYS 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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53A ILE* 4.1 2.1 - - - +
54A ASN* 4.0 12.1 - - - -
61A ASN* 2.9 39.5 + - - +
62A ALA 2.9 8.1 + - - +
64A GLY* 1.3 75.0 - - - +
66A ALA* 1.3 58.2 + - - +
68A HIS* 3.3 5.2 + - - +
69A ALA 3.1 20.1 + - - -
81A ALA* 3.7 19.2 - - - +
160A ASP 4.4 1.1 - - - +
161A VAL* 3.4 25.1 - - + +
162A GLN* 3.8 30.5 - - + -
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Residues in contact with ALA 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 ALA 3.0 14.6 + - - +
63A SER 3.8 4.3 - - - +
65A CYS* 1.3 73.5 - - - +
67A LEU* 1.3 66.3 + - - +
68A HIS 3.0 1.6 - - - -
69A ALA* 3.1 17.5 + - - +
70A CYS* 3.2 17.8 + - - -
137A MET* 3.6 15.9 - - + -
146A TRP* 3.9 19.5 - - + +
147A ILE* 4.1 19.5 - - - +
148A ALA* 3.7 2.4 - - - +
160A ASP 5.1 1.7 + - - +
161A VAL* 4.5 3.1 - - - +
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Residues in contact with LEU 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 SER 3.2 12.5 + - - +
64A GLY 3.2 8.3 + - - +
66A ALA* 1.3 79.3 - - - +
68A HIS* 1.3 58.4 + - + +
70A CYS* 3.5 2.1 - - - +
71A MET* 3.1 32.3 + - + +
90A TYR* 3.9 23.3 - - + -
91A MET* 3.6 29.8 - - + -
94A PHE* 4.4 15.9 - - + -
137A MET* 3.5 20.4 - - + +
192A VAL* 5.4 0.9 - - + -
197A PHE* 4.2 21.8 - - + -
200A TYR* 4.0 24.0 - - + -
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Residues in contact with HIS 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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53A ILE* 3.6 23.3 - - + +
64A GLY 3.1 16.1 + - - +
65A CYS 3.5 9.0 - - - +
66A ALA 3.0 0.4 - - - -
67A LEU* 1.3 77.3 - - + +
69A ALA* 1.3 59.9 + - - +
71A MET* 3.3 7.0 - - - +
72A ALA* 3.0 22.7 + - - +
77A GLY 4.6 1.4 - - - +
78A VAL* 5.6 0.2 - - - -
79A ARG* 2.7 27.5 + - + +
80A GLU 3.1 23.6 - - - -
81A ALA* 3.2 11.7 - - - -
82A PRO* 3.6 7.4 - - + +
200A TYR* 3.0 33.3 + + - -
206A TRP* 3.7 24.3 - + - -
209A LYS* 4.0 6.1 - - + -
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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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49A LEU* 5.4 2.5 - - + -
53A ILE* 4.3 8.5 - - - -
65A CYS 3.1 12.4 + - - +
66A ALA* 3.1 3.1 + - - +
68A HIS* 1.3 73.9 - - - +
70A CYS* 1.3 67.1 + - - +
72A ALA* 3.1 4.3 + - - +
73A MET* 3.0 30.7 + - + +
148A ALA* 3.3 28.3 - - + -
159A LEU* 4.9 6.3 - - + +
161A VAL* 4.1 23.3 - - + -
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Residues in contact with CYS 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 ALA 3.2 13.9 + - - -
67A LEU 3.5 7.9 - - - +
69A ALA* 1.3 80.2 - - - +
71A MET* 1.3 56.2 + - - +
73A MET* 3.3 1.1 + - - +
74A LEU* 2.9 37.7 + - - +
135A VAL* 3.5 29.8 - - + -
136A VAL 3.7 21.3 - - - -
137A MET* 3.5 22.4 - - - -
148A ALA* 4.1 6.1 - - - -
197A PHE* 3.6 15.0 - - + -
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Residues in contact with MET 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 LEU* 3.1 17.7 + - + +
68A HIS* 3.3 14.1 - - - +
70A CYS* 1.3 81.9 - - - +
72A ALA* 1.3 60.6 + - - +
74A LEU* 3.4 0.6 + - - -
75A GLY 3.3 3.8 + - - -
76A TYR* 3.2 47.5 + - + +
77A GLY 3.9 2.0 - - - +
197A PHE* 3.2 58.1 - - + +
200A TYR* 3.9 25.6 - - + -
201A ALA* 5.1 1.3 - - - -
206A TRP* 3.6 41.5 - - + -
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Residues in contact with ALA 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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24A VAL* 5.6 6.4 - - - -
25A LYS 5.7 1.6 + - - -
49A LEU* 4.6 8.7 - - + -
53A ILE* 4.7 2.5 - - + -
68A HIS 3.0 12.6 + - - +
69A ALA* 3.1 6.9 + - - +
71A MET* 1.3 75.1 - - - +
73A MET* 1.3 67.4 + - - +
74A LEU 3.1 0.2 - - - -
75A GLY* 3.1 18.0 + - - +
77A GLY* 3.5 13.1 + - - +
78A VAL* 3.6 31.9 - - + -
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Residues in contact with MET 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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25A LYS* 5.5 4.9 + - - -
28A LEU* 4.1 13.0 - - + -
45A LEU* 4.1 22.9 - - + -
49A LEU* 4.4 20.0 - - + -
69A ALA* 3.0 17.1 + - - +
70A CYS* 3.6 0.4 - - - -
72A ALA* 1.3 80.8 - - - +
74A LEU* 1.3 59.0 + - - +
75A GLY 3.2 1.3 - - - -
133A GLY 4.1 5.5 - - - +
135A VAL* 3.6 20.9 - - + -
148A ALA* 6.3 0.4 - - + -
150A PHE* 3.7 58.5 - - + -
157A MET* 5.3 0.2 - - - -
159A LEU* 4.6 11.2 - - + -
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Residues in contact with LEU 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 CYS 2.9 23.3 + - - +
71A MET 3.4 0.4 + - - +
72A ALA 3.1 0.2 - - - -
73A MET* 1.3 78.6 - - - +
75A GLY* 1.3 58.8 + - - +
76A TYR* 3.5 25.3 + - + -
133A GLY 4.2 9.4 - - - +
134A SER* 4.6 2.2 - - - -
135A VAL* 3.4 41.1 - - + +
194A ASP* 5.7 6.5 - - - +
197A PHE* 3.3 47.3 - - + -
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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