Contacts of the helix formed by residues 75 - 91 (chain A) in PDB entry 2W93
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 GLY 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 1.3 68.1 - - - +
76A VAL* 1.3 59.7 + - - -
77A GLY 3.3 0.9 - - - -
78A GLU* 2.9 16.4 + - - +
79A LEU* 3.0 36.7 + - - +
115A HIS 3.9 6.1 - - - -
125A PHE* 3.6 29.4 - - - -
412B TRP* 4.0 9.2 - - - -
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Residues in contact with VAL 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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73A THR* 3.6 10.3 - - + -
74A PHE 2.8 6.9 + - - -
75A GLY* 1.3 72.1 - - - -
77A GLY* 1.3 62.3 + - - +
80A SER* 2.8 25.8 + - - -
115A HIS* 3.5 26.9 - - + +
83B ASN* 3.4 11.2 + - - -
412B TRP* 3.3 50.7 - - + +
414B SER* 3.7 14.4 - - - +
600B TPP 3.3 31.9 - - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.5 29.9 - - - +
72A THR* 3.6 12.9 - - - +
73A THR* 3.0 17.8 + - - -
76A VAL* 1.3 79.8 - - - +
78A GLU* 1.3 67.2 + - - +
80A SER* 3.1 13.5 + - - -
81A ALA 3.3 8.3 + - - -
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Residues in contact with GLU 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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72A THR* 3.3 18.0 + - - +
73A THR 3.1 4.8 + - - +
74A PHE* 3.5 11.3 - - - -
75A GLY* 2.9 31.6 + - - +
77A GLY* 1.3 75.4 - - - +
79A LEU* 1.3 65.3 - - + +
81A ALA* 3.0 12.1 + - - +
82A LEU* 3.3 20.5 - - + +
97A HIS* 3.7 15.7 - - + -
99A VAL* 3.6 10.9 - - + +
125A PHE* 3.3 31.6 - - + +
129A SER* 4.7 0.9 + - - -
164A TYR* 2.6 35.6 + - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 3.0 21.2 + - - +
78A GLU* 1.3 77.9 - - + +
80A SER* 1.3 62.6 + - - +
81A ALA 3.3 0.5 + - - -
82A LEU* 3.4 30.5 + - + +
125A PHE* 3.7 38.1 - - + +
128A MET* 3.7 32.1 - - + -
79B LEU 4.4 7.4 - - - +
80B SER 5.6 0.3 - - - +
82B LEU* 4.3 8.5 - - + +
83B ASN* 3.9 22.0 + - + +
86B ALA* 3.5 32.5 - - + -
412B TRP* 4.2 2.9 - - + -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.7 21.3 + - - -
52A LEU* 3.5 28.0 - - - +
76A VAL 2.8 18.4 + - - -
77A GLY 3.1 10.9 + - - -
79A LEU* 1.3 79.2 - - - +
81A ALA* 1.3 60.9 + - - +
82A LEU 3.5 0.5 + - - -
83A ASN* 4.7 1.0 + - - +
52B LEU* 4.1 17.1 - - - +
56B TYR* 4.5 0.2 + - - -
79B LEU 5.5 1.2 - - - +
80B SER* 5.3 6.4 - - - +
83B ASN* 3.0 23.6 + - - +
600B TPP 4.3 2.4 - - - +
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Residues in contact with ALA 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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51A GLU 3.9 21.1 - - - +
52A LEU* 4.3 1.6 - - - +
55A ALA* 3.5 10.1 - - + +
70A ILE* 4.2 10.1 - - + -
72A THR* 4.4 2.5 - - + -
77A GLY 3.3 9.5 + - - +
78A GLU 3.0 11.1 + - - +
80A SER* 1.3 78.1 - - - +
82A LEU* 1.3 57.9 + - - +
83A ASN 3.3 1.1 - - - -
84A GLY* 2.9 22.4 + - - -
85A ILE* 3.0 11.5 + - + +
97A HIS* 4.1 17.3 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.3 22.9 - - - +
79A LEU* 3.4 32.0 + - + +
80A SER 3.4 3.2 - - - -
81A ALA* 1.3 78.9 - - - +
83A ASN* 1.3 57.3 + - - +
85A ILE* 3.2 12.5 + - + -
86A ALA* 2.8 31.9 + - - +
97A HIS* 4.4 4.5 - - + -
128A MET* 4.5 10.5 - - + -
129A SER* 3.3 27.6 - - - +
132A ILE* 3.6 16.3 - - + +
79B LEU* 4.6 10.8 - - + +
82B LEU* 5.6 3.6 - - + -
128B MET* 3.7 27.6 - - + -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 8.4 - - + +
56A TYR* 3.0 16.1 + - - -
80A SER 4.7 0.6 + - - -
81A ALA 3.2 1.0 + - - -
82A LEU* 1.3 76.9 - - - +
84A GLY* 1.3 61.7 + - - +
86A ALA* 4.4 1.6 - - - -
87A GLY* 3.2 16.1 + - - -
412A TRP* 3.0 34.6 + - - -
414A SER* 2.9 27.3 + - - -
75B GLY 3.9 1.9 - - - +
76B VAL* 3.4 14.9 + - - -
79B LEU* 3.9 12.5 + - + +
80B SER* 3.1 37.3 + - - +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.5 6.2 - - - +
55A ALA* 3.7 20.6 - - - +
56A TYR* 4.0 21.2 - - - -
59A ASP* 4.6 2.3 - - - +
81A ALA 2.9 8.8 + - - -
83A ASN* 1.3 76.8 - - - +
85A ILE* 1.3 64.8 + - - +
87A GLY* 3.2 3.7 + - - -
88A SER* 3.1 24.3 + - - -
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Residues in contact with ILE 85 (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 ALA* 4.6 7.6 - - + +
70A ILE* 4.3 6.5 - - + -
81A ALA* 3.0 18.4 + - + +
82A LEU* 3.2 10.3 + - + +
84A GLY* 1.3 74.6 - - - +
86A ALA* 1.3 56.7 + - - +
88A SER* 3.0 10.2 + - - +
89A TYR* 2.8 25.3 + - - +
95A VAL* 4.1 24.0 - - + -
97A HIS* 3.8 41.5 - - + +
129A SER* 5.5 1.8 - - - +
132A ILE* 3.8 26.2 - - + +
133A SER* 4.9 4.0 - - - +
162A PRO* 3.5 21.5 - - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 2.8 20.4 + - - +
83A ASN 3.9 1.3 - - - +
85A ILE* 1.3 72.7 - - - +
87A GLY* 1.3 57.9 + - - +
89A TYR* 3.1 3.8 + - - +
90A ALA* 2.8 29.3 + - - +
132A ILE* 3.8 24.2 - - + +
412A TRP* 3.6 16.6 - - + -
79B LEU* 3.4 26.9 - - + -
117B LEU* 3.8 5.1 - - + +
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Residues in contact with GLY 87 (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 ASP* 4.2 5.6 - - - +
83A ASN 3.2 6.2 + - - -
84A GLY 3.2 7.1 + - - -
86A ALA* 1.3 78.1 - - - +
88A SER* 1.3 56.9 + - - +
90A ALA* 4.3 0.2 - - - -
91A GLU* 3.0 35.0 + - - +
409A GLN* 4.1 6.0 + - - -
412A TRP* 3.3 34.9 - - - +
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Residues in contact with SER 88 (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 ALA 4.8 0.5 + - - -
59A ASP* 2.6 35.5 + - - +
84A GLY 3.1 11.1 + - - -
85A ILE* 3.0 11.4 + - - -
87A GLY* 1.3 75.0 - - - +
89A TYR* 1.3 65.5 + - - +
92A HIS* 3.0 4.3 + - - -
93A VAL* 2.8 40.6 + - - +
95A VAL* 3.6 12.0 - - - +
162A PRO* 3.6 15.6 - - - +
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Residues in contact with TYR 89 (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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85A ILE 2.8 9.5 + - - +
86A ALA* 3.1 10.1 + - - +
88A SER* 1.3 74.8 - - - +
90A ALA* 1.3 63.4 + - - +
92A HIS 3.2 8.1 + - - -
131A ASN 5.1 4.9 - - - -
132A ILE* 3.4 30.1 - - - +
133A SER* 3.7 27.2 + - - -
134A GLU* 3.9 7.9 + - - -
161A ARG* 2.8 66.6 + - - +
162A PRO* 3.4 11.3 - - + +
117B LEU* 3.9 37.0 - - + -
119B ASN* 4.8 10.9 + - + -
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Residues in contact with ALA 90 (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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86A ALA 2.8 16.6 + - - +
87A GLY 3.8 4.3 - - - +
88A SER 3.3 0.2 - - - -
89A TYR* 1.3 79.2 - - - +
91A GLU* 1.3 58.3 + - + +
92A HIS* 3.6 12.3 + - - -
288A LEU* 4.2 1.4 - - - +
411A LEU* 3.3 20.4 - - + +
412A TRP* 3.8 20.2 - - + -
116B THR 3.5 24.5 - - - +
117B LEU* 4.0 18.6 - - - +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 2.8 31.7 + - - +
87A GLY 3.0 18.6 + - - +
90A ALA* 1.3 77.9 - - - +
92A HIS* 1.3 70.8 + - - +
93A VAL* 3.5 2.5 - - + -
224A ARG* 2.8 29.8 + - - +
247A MET* 3.4 21.3 - - + +
288A LEU* 4.2 8.2 - - - +
408A SER 4.2 0.5 - - - +
409A GLN* 3.2 24.6 - - + +
411A LEU* 2.9 14.6 + - + -
412A TRP* 2.8 33.7 + - + +
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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