Contacts of the strand formed by residues 29 - 44 (chain D) in PDB entry 6UWZ
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 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG* 4.2 10.8 - - + -
21D PRO* 4.0 34.3 - - + +
22D VAL* 3.8 18.8 - - + -
28D PHE* 1.3 74.9 - - - +
30D ASP* 1.3 57.8 + - - +
31D ILE* 3.6 20.7 + - + -
60D TRP* 4.3 11.9 - - + -
61D ILE 4.8 3.8 - - - +
86D TRP* 4.2 6.5 - - + -
155D LYS 2.9 14.9 + - - +
156D VAL* 3.4 11.0 - - + +
157D SER 2.6 34.6 + - - +
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Residues in contact with ASP 30 (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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28D PHE* 3.9 19.8 + - + -
29D VAL* 1.3 70.2 - - - +
31D ILE* 1.3 64.3 + - - +
32D THR* 3.8 11.1 + - - -
59D GLN 3.6 7.1 - - - +
60D TRP* 3.8 11.5 - - - +
61D ILE 5.0 0.7 + - - -
157D SER* 3.3 13.6 + - - +
159D SER* 3.1 26.6 + - - -
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Residues in contact with ILE 31 (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 VAL* 4.0 12.6 - - + -
30D ASP* 1.3 75.0 + - - +
32D THR* 1.3 59.8 + - - +
33D VAL* 3.3 21.9 + - + -
58D GLN* 4.2 24.7 - - + +
59D GLN 3.1 9.2 - - - +
60D TRP* 3.8 20.6 - - + -
86D TRP* 4.4 1.8 - - + -
88D PRO* 3.6 23.1 - - + -
90D LEU* 5.2 0.7 - - + -
156D VAL* 3.2 35.9 - - + -
157D SER 2.7 10.7 + - - +
158D ILE* 3.2 11.9 - - + +
159D SER 2.9 24.0 + - - -
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Residues in contact with THR 32 (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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30D ASP* 3.8 13.0 + - - -
31D ILE* 1.3 68.7 - - - +
33D VAL* 1.3 59.6 + - - +
57D ARG* 3.7 0.9 - - - +
58D GLN* 3.6 2.9 - - - -
59D GLN* 2.9 53.3 + - - +
159D SER* 3.3 11.9 - - - +
160D PRO 4.4 2.0 - - - +
161D GLU* 3.6 35.4 - - + +
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Residues in contact with VAL 33 (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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31D ILE* 3.9 21.5 - - + +
32D THR* 1.3 74.8 - - - +
34D GLY* 1.3 61.9 + - - +
56D LEU* 3.9 24.5 - - + -
57D ARG 3.4 5.4 - - - +
58D GLN* 4.9 0.4 - - + -
90D LEU* 3.7 28.3 - - + -
146D LEU* 5.0 4.5 - - + -
158D ILE* 4.1 15.5 - - + -
159D SER 2.7 12.1 + - - +
160D PRO* 3.3 4.0 - - - +
161D GLU* 2.5 34.7 + - - -
201D ILE* 4.0 13.2 - - + -
203D TYR* 3.6 13.5 + - + +
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Residues in contact with GLY 34 (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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33D VAL* 1.3 78.8 - - - +
35D LEU* 1.3 59.0 + - - -
56D LEU* 3.4 7.8 - - - +
57D ARG* 2.8 41.5 + - - +
161D GLU* 3.5 24.6 + - - -
203D TYR* 3.8 6.3 - - - -
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Residues in contact with LEU 35 (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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34D GLY* 1.3 73.6 - - - -
36D GLN* 1.3 61.8 + - - +
37D LEU 3.9 1.6 - - - +
54D VAL* 3.8 33.2 - - + -
55D ARG 3.6 2.2 - - - +
56D LEU* 3.8 22.7 - - + -
57D ARG* 4.9 1.3 - - - +
124D PHE* 4.1 10.1 - - + -
144D MET* 3.5 28.5 - - + -
146D LEU* 4.5 5.4 - - + -
161D GLU* 4.9 0.2 + - - -
165D PRO* 3.5 7.5 - - + +
166D ASP* 3.0 25.9 + - - +
203D TYR* 3.9 34.4 + - + -
205D PHE* 3.8 19.7 - - + -
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Residues in contact with GLN 36 (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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34D GLY 4.2 0.2 - - - -
35D LEU* 1.3 71.6 - - - +
37D LEU* 1.3 62.5 + - - +
38D ILE* 3.6 13.8 + - + +
54D VAL* 3.2 5.7 - - - -
55D ARG* 2.8 59.3 + - + +
57D ARG* 4.5 16.5 + - - +
119D THR* 5.1 1.6 + - - -
166D ASP* 2.8 40.7 + - + +
168D SER* 4.0 5.5 + - - -
169D THR* 3.5 23.7 + - - +
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Residues in contact with LEU 37 (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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35D LEU* 3.9 3.9 + - + +
36D GLN* 1.3 72.4 - - - +
38D ILE* 1.3 62.4 + - - +
39D GLN 4.0 8.1 - - - +
40D LEU* 5.0 3.6 - - + +
52D THR* 3.7 33.9 - - + -
53D ASN 3.8 5.8 - - - +
54D VAL* 3.7 13.9 - - + +
144D MET* 5.1 0.4 - - + -
165D PRO* 5.3 0.4 - - + +
166D ASP 3.1 13.6 + - - +
167D LEU* 3.9 18.6 - - + +
169D THR* 3.9 4.0 + - - +
170D PHE* 3.5 45.0 + - + +
178D MET* 4.6 7.0 - - + -
205D PHE* 3.8 37.7 - - + -
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Residues in contact with ILE 38 (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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93C MET 5.8 2.5 - - - +
36D GLN* 3.7 18.4 - - + +
37D LEU* 1.3 76.8 - - - +
39D GLN* 1.3 59.5 + - - +
53D ASN* 2.8 36.2 + - - +
55D ARG* 3.9 38.1 - - + +
169D THR* 3.4 30.6 - - - +
170D PHE* 3.3 3.4 - - - -
171D MET* 2.7 41.0 + - + +
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Residues in contact with GLN 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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95C ASN 3.6 22.0 + - - -
96C ASN* 3.7 21.2 + - - +
127C SER* 3.6 21.2 + - - -
37D LEU* 3.9 3.2 - - - +
38D ILE* 1.3 81.9 - - + +
40D LEU* 1.3 65.5 + - - +
41D ILE* 3.7 10.9 + - + +
52D THR* 3.6 2.3 - - - -
53D ASN* 3.0 44.3 + - + +
170D PHE* 3.8 11.2 - - - -
171D MET* 3.7 32.4 - - + +
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Residues in contact with LEU 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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37D LEU* 5.3 3.8 - - + -
39D GLN* 1.3 77.9 - - - +
41D ILE* 1.3 63.6 + - - +
42D SER 4.2 5.8 - - - +
43D VAL* 4.0 7.2 - - + -
50D VAL* 3.5 30.7 - - + -
51D GLU 3.6 7.2 - - - +
52D THR* 3.8 10.5 - - + +
170D PHE* 3.7 20.5 - - + -
171D MET 4.8 1.4 + - - -
173D SER* 3.7 24.5 + - - +
176D TRP* 3.8 32.1 - - + -
178D MET* 4.9 5.4 - - + -
207D MET* 3.6 28.5 - - + -
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Residues in contact with ILE 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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47C ILE* 5.7 1.9 - - - +
96C ASN* 3.6 43.3 - - - +
39D GLN* 4.0 19.7 - - + +
40D LEU* 1.3 76.6 - - - +
42D SER* 1.3 63.3 + - - +
51D GLU* 3.0 36.1 + - + +
52D THR 4.1 3.4 - - - -
53D ASN* 4.0 15.5 - - + +
123D ILE* 3.7 23.3 - - + -
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Residues in contact with SER 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 LEU* 3.6 4.7 - - - +
41D ILE* 1.3 85.6 - - - +
43D VAL* 1.3 71.3 + - - +
44D ASP* 3.9 12.7 + - - +
49D ILE 4.5 0.6 + - - -
50D VAL* 3.5 4.7 - - - +
51D GLU* 3.2 43.4 + - - +
176D TRP* 5.6 0.4 - - - -
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Residues in contact with VAL 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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40D LEU* 4.0 15.5 - - + -
42D SER* 1.3 82.8 + - - +
44D ASP* 1.3 57.5 + - - +
45D GLU* 2.9 29.2 - - + +
49D ILE 3.5 5.4 - - - +
50D VAL* 4.0 12.3 - - + -
130D ILE* 3.9 28.3 - - + -
142D CYS* 5.4 0.4 - - - -
176D TRP* 3.7 46.2 - - + +
207D MET* 4.0 12.8 - - - -
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Residues in contact with ASP 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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42D SER* 3.9 8.4 + - - +
43D VAL* 1.3 70.6 - - - +
45D GLU* 1.3 64.2 + - - +
46D VAL* 3.4 17.5 + - - +
47D ASN* 3.3 33.2 + - - +
48D GLN* 2.9 24.4 + - - -
49D ILE* 2.8 33.9 + - + +
130D ILE* 4.1 2.6 - - - +
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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