Contacts of the helix formed by residues 82 - 101 (chain A) in PDB entry 5D0Y
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 PHE 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLY 4.5 0.2 - - - +
81A PHE* 1.3 79.0 - - - +
83A ILE* 1.3 67.1 + - + +
84A GLY* 2.9 41.7 + - - -
85A PHE* 3.1 38.7 + + + -
129A TRP* 3.6 32.3 - + + -
132A MET* 4.5 21.5 - - + -
133A LEU* 3.6 29.6 - - + -
201A FOL 3.0 25.8 + - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 5.9 2.0 - - + -
81A PHE* 3.7 31.6 - - + -
82A PHE* 1.3 81.6 - - + +
84A GLY* 1.3 64.1 + - - +
86A THR* 3.2 24.9 - - + +
87A LEU* 3.5 6.8 + - - +
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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
----------------------------------------------------------
82A PHE* 2.9 17.8 + - - -
83A ILE* 1.3 78.5 - - - +
85A PHE* 1.3 52.1 - - - -
86A THR 2.9 5.4 - - - -
87A LEU* 2.7 26.3 + - - +
88A THR 3.1 5.5 + - - -
129A TRP* 2.9 37.8 + - - -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 4.1 4.9 - - - +
82A PHE* 3.1 12.7 + + + -
84A GLY* 1.3 74.4 - - - +
86A THR* 1.3 60.0 + - - +
88A THR* 3.5 5.7 - - - -
89A ALA* 3.1 22.5 + - - +
126A ASN* 3.8 32.3 - - + -
129A TRP* 3.6 26.0 - + + +
130A VAL* 4.3 5.8 - - + -
133A LEU* 3.5 29.8 - - + -
201A FOL 3.4 92.4 - + + +
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Residues in contact with THR 86 (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 ALA* 3.7 29.7 - - + +
68A ASP* 2.7 24.4 + - - +
69A LEU* 4.7 11.7 - - + -
81A PHE* 3.7 13.3 - - - -
82A PHE 3.8 0.5 + - - -
83A ILE* 3.2 23.3 + - + -
84A GLY 2.9 0.2 - - - -
85A PHE* 1.3 77.3 - - - +
87A LEU* 1.3 65.8 + - - +
89A ALA* 3.3 4.2 + - - +
90A ALA* 3.2 20.3 + - - +
201A FOL 3.5 8.8 + - - -
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Residues in contact with LEU 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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61A PHE* 4.1 23.8 - - + -
83A ILE 3.5 5.6 + - - +
84A GLY* 2.7 13.2 + - - +
86A THR* 1.3 79.3 - - - +
88A THR* 1.3 59.8 + - - +
90A ALA* 3.0 7.5 + - - +
91A LEU* 2.9 46.7 + - + +
125A LEU* 4.5 4.5 - - + -
129A TRP* 4.4 18.8 - - + -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 3.1 2.0 + - - -
85A PHE* 3.5 10.3 - - - +
87A LEU* 1.3 77.8 - - - +
89A ALA* 1.3 54.5 + - - +
91A LEU* 3.2 5.2 + - - +
92A GLU* 2.7 42.4 + - + +
121A CYS* 3.9 24.0 - - + +
122A TYR* 5.2 3.6 - - + -
125A LEU* 3.8 14.2 - - - +
126A ASN* 2.9 29.7 + - - +
129A TRP* 2.9 28.1 + - - -
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Residues in contact with ALA 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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26A LYS* 4.4 17.1 + - - +
64A GLY* 3.4 30.7 - - - +
68A ASP* 4.1 15.3 - - + +
85A PHE 3.1 14.0 + - - +
86A THR 3.3 4.0 + - - +
88A THR* 1.3 79.5 - - - +
90A ALA* 1.3 59.3 + - - +
92A GLU* 3.8 14.0 - - - +
93A SER* 3.5 14.0 + - - -
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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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61A PHE* 3.3 56.2 - - + +
64A GLY* 4.2 0.4 - - - -
65A ALA* 3.7 11.0 - - + +
86A THR 3.2 10.9 + - - +
87A LEU* 3.0 11.8 + - - +
89A ALA* 1.3 77.3 - - - +
91A LEU* 1.3 59.3 + - - +
93A SER* 3.5 1.0 + - - -
94A MET* 3.0 27.9 + - - +
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Residues in contact with LEU 91 (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 PHE* 3.7 21.1 - - + -
87A LEU* 2.9 32.4 + - + +
88A THR* 3.9 2.9 - - - +
90A ALA* 1.3 72.4 - - - +
92A GLU* 1.3 67.7 + - - +
94A MET* 3.0 22.3 + - + -
95A ILE* 2.8 33.4 + - + +
120A ILE* 5.3 7.4 - - + -
121A CYS* 4.0 12.3 - - - -
125A LEU* 3.6 31.4 - - + -
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Residues in contact with GLU 92 (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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26A LYS* 3.7 18.2 + - - -
44A GLY 5.1 0.2 - - - -
45A PHE* 4.0 9.5 + - - -
48A SER* 3.4 22.7 + - - +
88A THR* 2.7 23.3 + - + +
89A ALA* 3.8 12.7 - - - +
91A LEU* 1.3 75.2 - - - +
93A SER* 1.3 59.0 + - - +
96A TYR* 3.0 36.6 + - + -
117A VAL* 4.1 11.1 - - + +
121A CYS* 3.6 14.7 - - + -
122A TYR* 2.6 37.9 + - + +
201A FOL 5.4 2.3 - - - +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 2.5 41.9 + - - +
51A LEU* 3.3 12.8 - - - +
52A GLY* 3.4 25.5 - - - -
56A GLY 4.5 0.3 - - - +
60A GLY* 3.1 28.4 - - - -
64A GLY* 4.3 2.3 - - - -
89A ALA 3.5 13.3 + - - -
90A ALA 3.5 2.0 + - - -
91A LEU 3.2 0.6 - - - -
92A GLU* 1.3 79.4 - - - +
94A MET* 1.3 58.3 + - - +
95A ILE 3.5 0.2 - - - -
96A TYR* 4.1 0.8 + - - -
97A GLY* 3.6 2.4 + - - -
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Residues in contact with MET 94 (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* 3.3 40.3 - - + +
58A TRP* 4.8 11.0 - - - -
60A GLY 4.4 0.2 + - - -
61A PHE* 3.8 19.1 - - + -
90A ALA 3.0 18.6 + - - +
91A LEU* 3.0 25.5 + - + +
93A SER* 1.3 78.0 - - - +
95A ILE* 1.3 71.3 + - + +
97A GLY* 3.4 2.4 + - - -
98A PHE* 3.2 44.7 + - + -
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Residues in contact with ILE 95 (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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91A LEU* 2.8 26.9 + - + +
94A MET* 1.3 81.5 - - + +
96A TYR* 1.3 63.8 + - - +
97A GLY 2.9 6.0 + - - -
98A PHE* 3.2 16.1 + - + +
99A PHE* 3.2 39.9 - - + -
113A SER* 4.4 1.3 - - - +
116A CYS* 4.1 9.4 - - + +
117A VAL* 3.8 26.0 - - + -
120A ILE* 4.1 28.7 - - + -
121A CYS* 4.3 19.1 - - - -
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Residues in contact with TYR 96 (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* 4.7 3.7 - - + +
48A SER* 3.9 13.0 - - - -
49A VAL* 3.5 44.3 - - + +
52A GLY* 4.1 6.7 - - - +
92A GLU* 3.0 28.7 + - + +
93A SER 4.3 4.7 - - - +
94A MET 3.5 0.2 - - - -
95A ILE* 1.3 78.4 - - - +
97A GLY* 1.3 56.5 + - - +
99A PHE* 4.7 1.6 - - - -
100A LEU* 2.9 59.1 + - + +
113A SER* 3.9 17.0 - - - -
114A VAL* 4.0 24.3 - - + +
117A VAL* 3.4 38.8 - - + +
122A TYR* 4.4 3.0 + - - -
156A HIS* 4.3 13.5 + - - -
160A VAL* 4.3 4.9 - - + +
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Residues in contact with GLY 97 (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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52A GLY* 3.5 22.0 - - - -
57A PRO* 4.2 14.8 - - - -
93A SER 3.6 6.6 + - - -
94A MET 3.4 8.4 + - - -
95A ILE 2.9 2.0 - - - -
96A TYR* 1.3 74.2 - - - +
98A PHE* 1.3 58.0 + - - -
99A PHE 2.8 10.9 + - - -
101A TYR* 3.0 28.9 + - - +
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Residues in contact with PHE 98 (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* 3.5 31.0 - - + -
58A TRP* 4.1 26.2 - + - -
94A MET* 3.2 34.0 + - + -
95A ILE* 3.2 12.5 + - + +
97A GLY* 1.3 72.9 - - - +
99A PHE* 1.3 66.3 + - + +
101A TYR 5.0 0.2 - - - -
103A LYS* 4.5 10.8 - - - -
109A ARG* 5.4 0.5 + - - -
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Residues in contact with PHE 99 (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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95A ILE* 3.2 33.8 + - + +
96A TYR 4.1 0.7 - - - +
97A GLY 2.8 2.0 + - - -
98A PHE* 1.3 87.2 - - + +
100A LEU* 1.3 60.1 + - + +
101A TYR 3.6 0.7 - - - -
103A LYS* 3.4 13.6 - - - +
108A TRP* 4.7 15.3 - + - -
109A ARG* 3.3 33.9 + - + +
112A ALA* 3.6 26.2 - - + -
113A SER* 3.7 27.8 - - - -
116A CYS* 3.6 34.1 - - + -
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Residues in contact with LEU 100 (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 VAL* 4.3 10.8 - - + +
52A GLY 4.7 0.4 - - - -
53A TYR* 3.4 31.8 - - + -
96A TYR* 2.9 58.4 + - + +
99A PHE* 1.3 80.3 - - + +
101A TYR* 1.3 62.1 + - - +
102A LYS 3.5 1.2 + - - -
103A LYS* 3.9 10.4 + - - +
109A ARG* 4.8 14.1 - - + +
110A VAL* 4.6 9.2 - - + -
113A SER* 4.0 11.4 - - - +
160A VAL* 4.5 8.1 - - + -
164A LEU* 3.4 37.4 - - + +
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Residues in contact with TYR 101 (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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52A GLY 3.6 10.1 - - - +
53A TYR 3.1 18.4 - - - -
54A LEU 3.5 21.5 + - - -
55A PHE 4.3 4.2 + - - -
56A GLY* 3.5 26.0 - - - -
57A PRO* 4.2 8.5 - - + -
96A TYR 4.2 0.2 + - - -
97A GLY 3.0 21.9 + - - +
98A PHE 5.0 0.2 - - - -
99A PHE 3.6 1.6 - - - -
100A LEU* 1.3 73.3 - - - +
102A LYS* 1.3 109.8 + - + +
103A LYS* 3.4 13.9 + - - +
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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