Contacts of the strand formed by residues 31 - 46 (chain A) in PDB entry 1UXU
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 LEU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.1 11.4 - - + -
23A PRO* 3.6 38.1 - - + +
24A VAL* 4.0 17.0 - - + -
30A VAL* 1.3 72.6 - - - +
32A ASN* 1.3 69.8 + - - +
33A VAL* 3.5 26.6 + - + -
62A TRP* 3.8 7.4 - - + -
63A HIS 3.7 16.6 - - - +
88A TRP* 3.8 19.1 - - + -
157A GLN 2.9 17.6 + - - +
158A VAL* 3.3 6.2 - - + +
159A ASP 2.9 23.0 + - - +
2214A NAG 5.2 0.7 - - - -
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Residues in contact with ASN 32 (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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30A VAL* 3.8 7.9 - - - +
31A LEU* 1.3 74.3 - - - +
33A VAL* 1.3 60.3 + - - +
34A THR* 5.9 1.6 - - + -
61A ILE 4.0 0.2 - - - +
62A TRP* 3.3 23.0 - - - +
63A HIS 4.4 2.1 + - - -
159A ASP* 3.4 14.5 - - - +
161A PHE* 3.3 21.7 - - + -
2214A NAG 1.4 69.1 + - - +
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Residues in contact with VAL 33 (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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31A LEU* 3.5 22.2 - - + -
32A ASN* 1.3 78.9 - - - +
34A THR* 1.3 77.5 + - - +
60A GLN* 4.1 10.1 - - + -
61A ILE 3.4 10.3 - - - +
62A TRP* 3.9 2.2 - - + -
90A PRO* 3.8 27.4 - - + -
92A ILE* 4.1 18.8 - - + -
158A VAL* 3.7 20.9 - - + -
159A ASP 2.8 11.1 + - - +
160A ILE* 3.3 5.3 - - - +
161A PHE* 2.8 26.5 + - - -
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Residues in contact with THR 34 (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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32A ASN* 5.9 1.6 - - + -
33A VAL* 1.3 80.7 - - - +
35A LEU* 1.3 60.2 + - - +
59A ARG 3.6 0.7 - - - +
60A GLN* 3.3 6.6 - - - -
61A ILE* 2.9 56.7 + - + +
161A PHE* 3.3 20.9 - - + -
162A ASN 5.1 0.7 - - - +
163A ALA* 4.3 18.7 - - - +
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Residues in contact with LEU 35 (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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34A THR* 1.3 74.3 - - - +
36A GLN* 1.3 68.6 + - - +
37A ILE* 3.5 35.8 + - + +
58A ILE* 4.0 13.2 - - + -
59A ARG 3.5 2.9 - - - +
60A GLN* 4.7 4.7 - - + +
92A ILE* 3.8 16.8 - - + -
148A PHE* 3.8 17.5 - - + -
160A ILE* 3.6 30.1 - - + -
161A PHE 2.8 12.1 + - - +
162A ASN* 3.8 7.2 - - - +
163A ALA* 2.9 23.4 + - - -
164A LEU 4.5 0.7 + - - -
202A VAL* 3.8 15.0 - - + -
204A PHE* 4.3 7.2 - - + -
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Residues in contact with GLN 36 (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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35A LEU* 1.3 79.6 - - - +
37A ILE* 1.3 66.2 + - - +
38A THR* 3.8 6.4 + - - +
57A TRP 3.7 0.9 - - - +
58A ILE* 3.5 4.7 - - - -
59A ARG* 2.8 49.5 + - + +
163A ALA* 4.0 14.6 - - + +
164A LEU* 3.7 30.9 - - + +
168A ASP* 3.1 30.7 + - - +
204A PHE* 5.2 0.4 - - - -
1215A EPE 4.1 16.3 + - - -
1216A EDO 4.2 13.9 + - - -
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Residues in contact with ILE 37 (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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35A LEU* 3.5 15.5 - - + +
36A GLN* 1.3 74.3 - - - +
38A THR* 1.3 66.6 + - - +
39A LEU 4.5 0.2 - - - +
56A LEU* 4.2 15.9 - - + -
57A TRP 4.2 0.7 - - - +
58A ILE* 3.5 31.4 - - + -
146A LEU* 5.3 0.2 - - + -
148A PHE* 3.7 22.9 - - + -
166A SER 4.7 0.2 - - - +
167A GLY* 3.6 1.6 - - - -
168A ASP* 2.7 35.3 + - - +
183A MET* 3.9 24.9 - - + -
204A PHE* 3.4 41.3 - - + -
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Residues in contact with THR 38 (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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36A GLN* 3.8 5.0 + - - +
37A ILE* 1.3 77.0 - - - +
39A LEU* 1.3 65.2 + - - +
40A SER* 3.5 3.5 + - - +
56A LEU* 3.3 7.1 - - - +
57A TRP* 2.9 49.6 + - + -
168A ASP* 3.2 30.9 + - - +
171A ASP* 3.8 35.7 - - + +
1215A EPE 3.8 18.4 - - - -
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Residues in contact with LEU 39 (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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37A ILE* 4.1 1.8 - - - +
38A THR* 1.3 71.1 - - - +
40A SER* 1.3 61.1 + - - +
41A GLN 3.8 21.5 - - - +
42A ILE* 4.7 3.6 - - + +
54A ALA* 4.1 9.2 - - + -
55A TYR 3.8 1.1 - - - +
56A LEU* 3.6 24.2 - - + -
168A ASP 3.1 10.6 + - - +
169A LEU* 3.9 25.1 - - + -
171A ASP 4.2 1.2 - - - -
172A PHE* 3.3 49.8 + - + +
180A VAL* 4.2 5.6 - - + -
183A MET* 4.4 9.6 - - + -
206A LEU* 4.1 33.0 - - + -
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Residues in contact with SER 40 (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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38A THR* 3.5 3.4 + - - +
39A LEU* 1.3 73.8 - - - +
41A GLN* 1.3 62.6 + - - +
55A TYR* 2.8 31.5 + - - +
56A LEU 4.2 1.4 - - - -
57A TRP* 3.2 31.5 + - - -
171A ASP* 3.9 10.8 - - - +
172A PHE* 3.5 2.4 - - - -
173A ILE* 3.1 28.8 + - - +
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Residues in contact with GLN 41 (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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39A LEU* 3.6 6.1 - - - +
40A SER* 1.3 84.3 - - - +
42A ILE* 1.3 77.4 + - - +
43A LYS* 3.5 28.7 + - - +
54A ALA* 3.5 3.3 - - - -
55A TYR* 2.9 57.5 + - + +
172A PHE* 3.9 8.7 - - - -
173A ILE* 3.9 21.2 - - + +
174A GLU 6.1 0.2 - - - +
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Residues in contact with ILE 42 (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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39A LEU* 4.7 9.6 - - + -
41A GLN* 1.3 85.5 + - - +
43A LYS* 1.3 62.5 + - - +
44A ASP 4.0 13.5 - - - +
45A MET* 4.3 8.5 - - + +
52A LEU* 3.8 25.6 - - + -
53A THR 4.1 2.2 - - - -
54A ALA* 4.7 1.3 - - - +
172A PHE* 3.8 26.5 - - + -
173A ILE 5.0 0.8 + - - -
175A ASP* 3.6 39.2 - - + +
178A TRP* 4.4 9.4 - - + +
180A VAL* 4.4 2.9 - - + -
206A LEU* 5.2 1.8 - - + -
208A LEU* 3.8 33.7 - - + -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.5 23.9 + - - +
42A ILE* 1.3 75.4 - - - +
44A ASP* 1.3 63.4 + - + +
53A THR* 2.9 25.7 + - + +
55A TYR* 3.2 48.1 + - + +
175A ASP* 5.4 0.8 - - - +
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Residues in contact with ASP 44 (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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42A ILE* 3.5 5.5 - - - -
43A LYS* 1.3 84.9 - - + +
45A MET* 1.3 69.9 + - - +
46A ASP* 3.6 24.2 - - - +
51A ILE 3.6 1.1 - - - +
52A LEU* 3.5 4.5 - - - +
53A THR* 2.8 48.5 + - - +
175A ASP* 6.1 0.2 - - - -
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Residues in contact with MET 45 (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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42A ILE* 4.3 10.1 - - + +
44A ASP* 1.3 76.3 + - - +
46A ASP* 1.3 87.5 + - - +
47A GLU* 3.3 12.5 + - + +
50A GLN* 4.2 2.7 - - - -
51A ILE 3.8 11.0 - - - +
52A LEU* 4.3 5.8 - - + -
130A CYS* 3.9 29.2 - - + -
142A GLN* 3.9 30.7 - - + +
144A CYS* 4.0 8.7 - - - -
178A TRP* 3.5 50.1 + - + +
208A LEU* 4.2 7.6 - - + -
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Residues in contact with ASP 46 (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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44A ASP* 3.6 20.7 - - - +
45A MET* 1.3 71.9 - - - +
47A GLU* 1.3 53.2 + - - +
48A ARG* 3.0 22.2 + - - +
49A ASN* 2.8 34.6 + - - +
50A GLN* 2.7 31.5 + - - -
51A ILE* 2.9 31.0 + - + +
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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