Contacts of the strand formed by residues 33 - 44 (chain D) in PDB entry 3DXA
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 TYR 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA 5.1 0.7 + - - -
151A ARG* 4.2 11.9 + - - +
152A VAL* 5.7 0.3 - - - -
155A GLN* 3.2 41.5 - - + +
5C LEU* 4.3 13.2 - - + +
7C PHE* 4.5 12.8 - + - -
28D ILE* 4.4 0.4 - - - +
31D ASN 4.5 7.9 - - - -
32D GLU* 1.3 75.9 - - - +
39D VAL* 1.3 61.1 + - - +
40D TYR* 3.5 22.7 - + + -
55D HIS* 3.6 28.5 - + - -
56D GLY 4.2 2.5 - - - +
57D LEU* 3.6 40.2 - - + +
106D VAL* 3.5 6.9 - - - +
107D TRP* 2.7 55.0 + + - +
108D GLY 5.9 0.4 - - - -
109D GLY 5.1 1.8 - - - -
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Residues in contact with VAL 39 (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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25D HIS* 3.8 26.0 - - + +
28D ILE* 3.8 21.5 - - + -
32D GLU 5.0 0.7 - - - +
33D TYR* 1.3 71.0 - - - +
40D TYR* 1.3 63.0 - - - +
41D TRP* 4.0 16.6 - - + +
55D HIS* 3.2 17.0 - - - +
56D GLY 3.1 22.2 + - - +
57D LEU 5.0 0.4 + - - -
58D LYS* 5.0 4.0 - - + -
81D LEU* 4.0 5.6 - - + +
83D ILE* 4.1 17.7 - - + -
87D SER* 3.5 24.0 - - - +
104D CYS* 4.7 5.4 - - - -
105D ILE 4.1 3.1 - - - +
106D VAL* 4.8 2.5 - - + +
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Residues in contact with TYR 40 (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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7C PHE* 4.8 2.3 - - - -
33D TYR* 3.5 32.7 - + + -
39D VAL* 1.3 73.4 - - - +
41D TRP* 1.3 63.4 + - - +
42D TYR* 4.3 7.6 - + + -
52D TYR* 3.8 28.3 - + - -
54D ILE 3.9 1.8 - - - -
55D HIS* 3.5 28.0 + + + -
104D CYS* 3.7 3.1 - - - -
105D ILE* 2.8 53.9 + - + +
107D TRP* 3.7 31.9 - + + -
113E TYR* 3.6 4.7 - - - +
114E ASN* 3.0 51.2 + - + +
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Residues in contact with TRP 41 (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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6D GLN* 3.6 22.2 - - - -
21D LEU* 3.2 31.6 - - + -
22D PRO 3.7 11.7 - - - -
23D CYS* 3.6 20.6 - - + -
39D VAL* 4.0 12.1 - - + +
40D TYR* 1.3 79.1 - - - +
42D TYR* 1.3 66.9 + - - +
52D TYR* 4.5 0.3 - - - -
53D ILE* 3.1 25.5 + - + +
54D ILE* 2.9 26.6 + - + +
81D LEU* 4.1 23.3 - - + +
87D SER* 4.0 17.1 + - - -
89D LEU* 3.3 40.4 - - + +
102D TYR* 4.2 17.5 - - + -
103D TYR 3.4 15.3 - - - -
104D CYS* 3.6 6.4 - - + -
119D THR* 5.5 0.9 - - - -
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Residues in contact with TYR 42 (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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40D TYR* 4.3 9.8 - + - -
41D TRP* 1.3 82.5 - - - +
43D ARG* 1.3 57.3 + - - +
50D PRO* 3.9 14.4 - - + -
51D GLN 2.9 20.2 - - - -
52D TYR* 3.5 31.6 - + + -
53D ILE* 3.8 5.3 - - - +
102D TYR* 3.5 3.8 - - - +
103D TYR* 2.8 44.0 + - + +
105D ILE* 4.3 18.6 - - + +
113D VAL* 6.1 3.6 - - + -
115D PHE* 4.0 22.0 - + + -
114E ASN* 2.8 25.1 + - - -
115E GLU* 3.7 1.4 - - - -
116E GLN* 2.9 35.3 + - + +
118E PHE* 4.3 11.2 - + - -
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Residues in contact with ARG 43 (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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42D TYR* 1.3 72.0 - - - +
44D GLN* 1.3 62.2 + - - +
45D ILE* 3.9 26.5 + - + +
50D PRO* 3.3 3.2 - - - +
51D GLN* 3.0 57.2 + - + +
53D ILE* 3.3 24.4 - - + +
78D MET* 3.3 37.9 - - - +
91D LEU* 4.3 10.8 - - - +
97D ARG 5.3 0.6 + - - -
98D ASP* 3.9 23.0 + - - +
100D ALA* 4.1 7.2 - - + -
101D VAL 3.5 5.2 - - - -
102D TYR* 3.5 33.8 + - + -
103D TYR* 4.8 0.4 - - - -
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Residues in contact with GLN 44 (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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43D ARG* 1.3 74.1 - - - +
45D ILE* 1.3 57.2 + - - +
46D HIS* 2.9 14.6 + - - +
48D GLN 3.7 7.1 - - - +
49D GLY* 3.5 33.0 - - - +
50D PRO* 3.7 17.0 - - + +
100D ALA* 3.8 3.1 - - - -
101D VAL* 2.7 33.7 + - + +
103D TYR* 2.6 45.2 + - + +
44E GLN* 2.9 37.3 + - - +
50E PRO* 4.2 2.0 - - - +
103E LEU* 4.5 0.5 - - - +
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Residues in contact with ILE 45 (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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43D ARG* 3.9 27.5 + - + +
44D GLN* 1.3 68.0 - - - +
46D HIS* 1.3 56.8 + - + +
47D SER* 2.7 19.2 + - - -
48D GLN* 2.9 29.2 + - + +
49D GLY 4.6 3.4 - - - +
51D GLN* 3.3 27.8 - - - +
97D ARG 4.5 17.9 - - - +
99D THR 4.5 7.0 - - - +
100D ALA* 3.6 10.1 - - + -
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Residues in contact with HIS 46 (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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44D GLN* 2.9 17.3 + - - +
45D ILE* 1.3 71.8 - - + +
47D SER* 1.3 85.6 + - - +
48D GLN 3.0 13.9 - - - +
99D THR 5.3 2.4 + - - +
100D ALA* 4.7 3.6 - - - +
101D VAL* 5.7 2.9 - - - +
187E PRO* 3.3 43.0 + - + +
188E GLN* 3.7 24.8 + - - -
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Residues in contact with SER 47 (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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45D ILE 2.7 6.9 + - - -
46D HIS* 1.3 95.7 - - - +
48D GLN* 1.3 81.4 + - - +
120E PRO 5.5 2.3 - - - +
169E GLU* 5.1 5.9 + - - -
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Residues in contact with GLN 48 (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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44D GLN* 3.7 8.9 - - - +
45D ILE* 2.9 39.5 - - + +
46D HIS 3.0 13.3 - - - +
47D SER* 1.3 98.3 + - - +
49D GLY* 1.3 65.7 + - - +
44E GLN* 5.4 0.2 - - - +
120E PRO* 6.0 2.0 - - - -
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Residues in contact with GLY 49 (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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44D GLN* 3.5 14.3 - - - +
45D ILE 4.6 3.6 - - - +
48D GLN* 1.3 83.1 + - - +
50D PRO* 1.4 77.6 - - - +
103E LEU* 4.9 11.9 - - - -
118E PHE* 4.1 10.3 - - - +
119E GLY 5.3 3.5 - - - +
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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
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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