Contacts of the helix formed by residues 98 - 113 (chain D) in PDB entry 2W2X
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 VAL 98 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.4 31.0 - - + -
37A PHE* 4.3 10.1 - - + -
64A TYR* 4.0 18.6 - - + -
67A LEU* 3.7 18.8 - - + -
77D PHE* 3.3 43.8 - - + -
97D LYS* 2.5 45.1 + - - +
99D GLU* 1.3 83.3 + - - +
100D GLU 3.1 0.3 + - - -
101D LEU* 3.3 5.0 + - + +
102D PHE* 2.9 22.2 + - - +
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.0 12.6 - - - +
67A LEU* 4.0 18.2 + - - +
70A LEU* 3.8 26.1 - - + +
97D LYS* 4.0 26.7 - - + +
98D VAL* 1.3 100.1 + - - +
100D GLU* 1.3 68.9 + - - +
102D PHE* 3.9 3.5 - - - +
103D GLU* 3.4 25.1 + - - +
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU 6.0 2.0 - - - +
95D THR* 3.6 16.9 - - + -
96D ASP* 4.0 6.4 + - - +
97D LYS* 2.9 70.9 + - - +
99D GLU* 1.3 79.4 - - - +
101D LEU* 1.3 66.8 + - - +
102D PHE 3.1 1.7 + - - -
103D GLU* 3.1 6.0 + - - +
104D TRP* 2.8 36.6 + - + +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 5.9 0.9 - - + -
37A PHE* 4.3 8.7 - - + -
67D LYS* 3.9 27.6 - - + -
68D ALA 5.7 1.3 - - - +
76D SER 5.1 0.4 - - - +
77D PHE* 3.5 38.4 - - + +
78D VAL 3.8 31.2 - - - +
79D PHE* 3.9 19.7 - - + +
95D THR* 3.4 19.8 - - + +
97D LYS 3.3 2.4 + - - -
98D VAL* 3.3 9.6 + - + +
100D GLU* 1.3 75.9 - - - +
102D PHE* 1.3 62.9 + - - +
104D TRP* 4.7 1.6 - - - -
105D PHE* 2.9 30.7 + - + +
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Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.7 35.6 - + + -
56A TRP* 4.1 6.5 - + - -
67A LEU* 3.7 24.7 - - + -
70A LEU* 3.5 45.1 - - + -
71A SER* 3.6 22.2 - - - -
98D VAL 2.9 17.1 + - - +
99D GLU 3.9 5.2 - - - +
101D LEU* 1.3 77.6 - - - +
103D GLU* 1.3 72.8 + - + +
105D PHE* 3.8 0.5 - - - +
106D GLN* 3.1 62.3 + - + +
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Residues in contact with GLU 103 (chain D).
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* 5.8 5.5 - - + +
8D GLN* 3.4 28.4 + - - +
99D GLU 3.4 15.9 + - - +
100D GLU* 3.1 6.7 + - - +
102D PHE* 1.3 89.8 - - + +
104D TRP* 1.3 66.9 + - + +
106D GLN* 3.5 2.1 + - - +
107D SER* 3.2 21.1 + - - -
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Residues in contact with TRP 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN* 3.2 33.2 + - + -
9D GLN* 3.6 28.3 + - - -
10D GLY* 3.7 11.2 - - - -
11D GLU 4.7 4.4 + - - -
12D LEU* 3.7 33.5 - - + +
27D CYS* 3.8 26.9 - - + -
28D ALA* 4.0 6.7 - - - -
29D ILE* 3.5 29.4 - - + -
34D LEU* 3.9 13.0 - - + -
79D PHE* 3.9 15.7 - + + -
95D THR* 5.3 0.2 - - + -
100D GLU* 2.8 39.8 + - + +
101D LEU* 4.0 1.3 - - - +
103D GLU* 1.3 76.1 - - + +
105D PHE* 1.3 52.3 + - - +
107D SER* 3.2 3.6 + - - -
108D ILE* 2.8 50.1 + - + +
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Residues in contact with PHE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.0 15.7 - + + -
39A ASN* 4.1 16.8 - - + -
65D VAL* 3.6 39.2 - - + +
66D VAL* 4.0 0.4 - - - -
67D LYS* 3.6 42.0 - - + -
79D PHE* 4.4 8.8 - - + -
101D LEU* 2.9 23.9 + - + +
102D PHE* 3.8 3.4 - - - +
104D TRP* 1.3 77.2 - - - +
106D GLN* 1.3 65.6 + - - +
108D ILE* 3.1 3.2 + - - +
109D ARG* 2.7 64.1 + - + +
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.0 4.4 - - - -
39A ASN* 3.0 23.4 + - - -
56A TRP* 3.2 21.9 - - + -
102D PHE* 3.1 47.1 + - + +
103D GLU* 4.0 3.8 - - - +
104D TRP 3.2 0.2 + - - -
105D PHE* 1.3 85.4 - - - +
107D SER* 1.3 57.4 + - - +
109D ARG* 2.3 42.4 + - - +
110D GLU* 2.7 36.7 + - - +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN* 3.8 30.3 - - - -
29D ILE* 4.2 7.0 - - - -
103D GLU 3.2 12.6 + - - -
104D TRP 3.2 9.0 + - - -
106D GLN* 1.3 75.1 - - - +
108D ILE* 2.2 49.6 - - - +
110D GLU* 3.7 10.2 - - - +
111D ILE* 3.2 34.1 + - - +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 4.0 18.4 - - + -
34D LEU* 4.3 8.5 - - + -
60D LEU* 3.9 25.4 - - + -
65D VAL* 3.1 24.9 - - + -
79D PHE* 3.3 40.8 - - + -
81D LEU* 4.2 9.0 - - + -
104D TRP* 2.8 32.2 + - + +
105D PHE 3.1 1.7 + - - +
107D SER* 2.2 49.0 - - - +
109D ARG* 1.3 61.9 + - - +
110D GLU 3.2 1.8 - - - -
111D ILE* 2.8 10.9 + - - +
112D THR* 2.8 37.3 + - + -
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 3.8 21.5 - - - +
56A TRP* 3.6 24.5 - - - +
65D VAL* 3.4 14.9 - - + +
105D PHE* 2.7 39.4 + - + +
106D GLN* 2.3 44.3 + - - +
108D ILE* 1.3 77.7 - - - +
110D GLU* 1.3 68.5 + - - +
112D THR* 3.8 2.7 - - - -
113D TRP* 2.9 62.3 + - + +
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLN 2.7 22.7 + - - +
107D SER* 3.7 11.9 - - - +
109D ARG* 1.3 80.9 - - - +
111D ILE* 1.3 62.4 + - - +
113D TRP* 3.4 19.7 - - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 3.8 18.4 - - + -
31D ASP 3.0 28.3 - - - +
32D ALA* 3.9 17.0 - - + -
60D LEU* 3.8 37.2 - - + -
61D ASN* 4.9 7.6 - - - +
107D SER* 3.2 27.1 + - - +
108D ILE* 2.8 10.8 + - - +
110D GLU* 1.3 81.0 - - - +
112D THR* 1.3 60.8 + - + +
113D TRP 3.5 4.0 + - - +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.7 14.6 - - + +
61D ASN* 6.1 1.3 - - - +
63D TYR* 3.2 32.3 - - + +
64D ASN* 4.3 13.9 + - - +
65D VAL* 3.8 12.9 + - + +
84D LYS* 5.7 2.6 + - - -
108D ILE* 2.8 37.9 + - + +
109D ARG* 3.4 13.5 + - - -
111D ILE* 1.3 75.2 - - + +
113D TRP* 1.3 69.0 + - - +
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Residues in contact with TRP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 6.4 1.1 - - + -
40A TYR 5.7 1.6 - - - -
41A SER* 3.7 34.3 - - - -
52A ASN* 5.7 6.3 - - - -
109D ARG* 2.9 60.1 + - + +
110D GLU* 3.4 14.8 - - - +
111D ILE 3.4 3.7 - - - +
112D THR* 1.3 88.0 + - - +
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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