Contacts of the helix formed by residues 77 - 93 (chain A) in PDB entry 2DXU
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 LYS 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS 4.9 2.7 - - - +
74A ASP* 2.8 46.7 + - - +
75A LEU 3.0 2.0 + - - -
76A PRO* 1.3 76.8 - - + +
78A ILE* 1.3 66.8 + - - +
79A VAL 3.2 3.1 - - - -
80A PHE* 3.0 39.5 + - + +
81A LEU* 3.5 6.8 + - - +
171A PHE* 4.0 10.8 - - + -
175A PRO 2.7 28.4 + - - +
176A MET* 3.3 22.0 - - - +
178A ILE* 4.1 5.4 - - + +
179A LEU* 3.7 27.6 - - + +
209A ASP 5.1 1.4 + - - +
210A PHE* 4.8 11.2 - - - +
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Residues in contact with ILE 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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66A LEU* 3.9 23.3 - - + -
68A PRO* 4.1 22.0 - - + -
74A ASP 4.4 0.2 + - - -
75A LEU* 3.2 24.3 + - + +
76A PRO 3.3 0.2 - - - -
77A LYS* 1.3 78.7 - - - +
79A VAL* 1.3 64.4 + - - +
81A LEU* 2.9 35.3 + - + +
82A GLY 3.4 3.3 + - - -
117A VAL* 4.2 24.9 - - + -
124A ILE* 4.3 9.9 - - + -
126A LEU* 4.0 10.2 - - + +
168A TYR* 4.6 0.4 - - + -
171A PHE* 3.4 33.2 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO 3.6 7.7 + - - +
78A ILE* 1.3 77.8 - - - +
80A PHE* 1.3 81.7 + - + +
82A GLY* 3.2 4.3 + - - -
83A ALA* 3.1 18.9 + - - +
102A PRO* 3.8 8.3 - - + +
103A ASN* 3.6 31.0 - - + -
115A VAL* 3.7 16.6 - - + +
117A VAL* 3.6 22.8 - - + +
227A TYR* 3.6 34.9 + - + +
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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
----------------------------------------------------------
76A PRO 4.6 3.8 - - - -
77A LYS* 3.0 37.1 + - + +
79A VAL* 1.3 80.4 - - + +
81A LEU* 1.3 60.5 + - - +
83A ALA* 4.3 6.1 - - + -
84A VAL* 2.9 34.3 + - - +
99A ILE* 5.8 1.8 - - + -
101A TRP* 3.9 15.3 - + - -
102A PRO* 3.7 33.4 - - + -
178A ILE* 3.8 9.6 - - + -
179A LEU* 4.0 13.9 - - + -
182A VAL* 3.4 33.7 - - + -
207A ILE* 5.5 1.3 - - + -
210A PHE 5.2 0.4 - - - -
211A GLY* 3.8 36.8 - - - -
227A TYR* 5.2 5.8 - + - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 5.2 2.2 - - + -
77A LYS 4.1 6.3 - - - +
78A ILE* 2.9 42.1 + - + +
80A PHE* 1.3 77.0 - - - +
82A GLY* 1.3 58.3 + - - +
85A GLY* 2.9 23.4 + - - -
126A LEU* 4.8 5.8 - - + -
164A LEU* 3.4 13.3 - - + +
167A LEU* 3.8 33.6 - - + +
168A TYR* 4.0 25.4 - - + +
171A PHE* 3.9 18.4 - - + -
178A ILE* 3.8 30.1 - - + -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE 3.4 4.0 + - - -
79A VAL 3.2 6.9 + - - -
81A LEU* 1.3 80.3 - - - +
83A ALA* 1.3 61.2 + - - +
85A GLY* 3.3 1.4 + - - -
86A VAL* 3.0 28.3 + - - +
115A VAL* 3.9 8.7 - - - -
126A LEU* 4.2 11.9 - - - +
128A ILE* 4.0 21.0 - - - +
164A LEU* 4.0 4.7 - - - -
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Residues in contact with ALA 83 (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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79A VAL 3.1 15.2 + - - +
80A PHE* 3.9 7.6 - - + +
82A GLY* 1.3 77.0 - - - +
84A VAL* 1.3 62.1 + - - +
86A VAL* 3.3 4.6 + - - +
87A VAL* 3.0 25.8 + - - +
99A ILE* 3.8 31.6 - - + -
102A PRO 4.5 8.3 - - - +
103A ASN 5.0 2.9 - - - -
105A VAL* 3.9 10.3 - - + +
115A VAL* 3.7 14.2 - - + +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 2.9 19.1 + - - +
81A LEU 4.2 1.3 - - - +
83A ALA* 1.3 72.6 - - - +
85A GLY* 1.3 66.8 + - - +
87A VAL* 3.2 5.4 + - + +
88A GLU* 2.9 45.2 + - + +
99A ILE* 4.0 12.8 - - + -
167A LEU* 4.0 11.0 - - + -
178A ILE* 3.8 16.8 - - + -
181A LEU* 4.1 17.9 - - + +
182A VAL* 3.8 28.3 - - + +
185A ASN* 4.9 7.4 - - - +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 2.9 16.0 + - - -
82A GLY 3.8 0.9 - - - -
84A VAL* 1.3 76.1 - - - +
86A VAL* 1.3 61.7 + - - +
88A GLU* 3.4 5.8 + - - +
89A THR* 3.0 26.2 + - - -
160A LEU* 3.5 8.5 - - - +
163A ASN* 4.0 5.5 + - - -
164A LEU* 4.0 10.3 - - - -
167A LEU* 3.6 19.2 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 3.0 18.6 + - - +
83A ALA* 3.6 7.4 - - - +
84A VAL 3.2 0.2 - - - -
85A GLY* 1.3 77.0 - - - +
87A VAL* 1.3 58.0 + - - +
89A THR* 3.2 4.7 + - - -
90A LEU* 2.9 47.3 + - + +
105A VAL* 3.9 17.7 - - + -
113A ALA* 3.9 17.7 - - + -
115A VAL* 5.1 2.5 - - + -
128A ILE* 3.6 29.6 - - + -
130A LEU* 4.2 12.3 - - + -
160A LEU* 4.0 14.1 - - + -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.0 19.1 + - - +
84A VAL* 3.2 9.2 + - - +
86A VAL* 1.3 75.7 - - - +
88A GLU* 1.3 59.9 + - + +
90A LEU* 3.2 9.4 + - - +
91A LYS* 2.9 39.6 + - + +
97A GLY 3.6 24.7 - - - +
99A ILE* 3.7 26.2 - - + +
105A VAL* 4.0 14.6 - - + -
185A ASN* 3.6 30.1 - - + +
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Residues in contact with GLU 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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84A VAL* 2.9 37.3 + - + +
85A GLY 3.8 1.6 - - - +
87A VAL* 1.3 78.3 - - + +
89A THR* 1.3 62.9 + - - +
91A LYS* 3.3 11.1 + - + +
92A GLU* 3.1 26.4 + - - +
163A ASN* 3.6 16.9 - - - +
166A ARG* 3.0 28.0 + - - +
167A LEU* 3.6 23.1 - - - +
181A LEU* 4.4 8.3 - - - +
185A ASN* 5.8 2.9 - - - +
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Residues in contact with THR 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 GLY 3.0 12.4 + - - -
86A VAL* 3.6 5.2 - - - +
88A GLU* 1.3 77.8 - - - +
90A LEU* 1.3 63.7 + - - +
92A GLU* 3.1 10.9 + - - +
93A PHE* 3.1 32.1 - - + -
130A LEU* 5.1 6.5 - - + -
143A MET* 5.1 1.8 - - + -
156A VAL* 4.0 21.8 - - + +
159A SER* 2.9 32.4 + - - +
160A LEU* 3.2 22.0 - - + +
163A ASN* 3.0 11.7 + - - +
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Residues in contact with LEU 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 VAL* 2.9 28.3 + - + +
87A VAL* 3.6 4.7 - - - +
89A THR* 1.3 78.3 - - + +
91A LYS* 1.3 57.1 + - - +
93A PHE* 2.9 17.6 + - - +
95A ILE* 2.8 45.3 + - + +
97A GLY* 3.9 12.6 - - - +
105A VAL* 3.7 30.3 - - + -
112A ILE* 3.9 22.7 - - + -
130A LEU* 4.3 8.1 - - + -
143A MET* 3.8 36.1 - - + -
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Residues in contact with LYS 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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87A VAL* 2.9 37.6 + - + +
88A GLU* 3.7 10.1 - - + +
89A THR 3.2 0.2 - - - -
90A LEU* 1.3 75.7 - - - +
92A GLU* 1.3 59.6 + - - +
94A SER* 2.9 20.4 + - - +
95A ILE 3.8 12.8 - - - +
96A ASP* 5.5 2.0 - - - +
97A GLY 5.2 3.1 - - - +
185A ASN* 4.4 9.6 - - - +
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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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88A GLU* 3.1 14.1 + - - +
89A THR 3.1 8.3 + - - +
91A LYS* 1.3 77.0 - - - +
93A PHE* 1.3 66.0 + - + +
94A SER* 3.3 3.4 + - - -
159A SER* 2.7 28.8 + - - +
163A ASN* 2.9 33.5 + - - +
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Residues in contact with PHE 93 (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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89A THR* 3.1 36.1 + - + -
90A LEU 2.9 8.9 + - - +
92A GLU* 1.3 82.2 - - + +
94A SER* 1.3 70.2 + - - +
95A ILE* 3.3 3.8 + - + +
143A MET* 3.6 21.1 - - + -
147A LEU* 3.4 23.3 - - + +
151A VAL* 3.4 32.1 - - + -
152A PRO* 5.3 1.3 - - + -
155A SER* 4.0 15.5 - - - -
156A VAL* 3.9 24.7 - - + -
159A SER* 4.1 13.5 - - - -
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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
------------------------------------------------------------
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