Contacts of the strand formed by residues 27 - 42 (chain C) in PDB entry 3U8M
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 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.5 30.5 - - + -
20C PRO* 3.6 33.4 - - + +
21C THR* 3.9 4.5 - - - +
22C GLN 6.1 0.2 - - - +
25C ARG 3.7 0.2 + - - -
26C PRO* 1.3 70.0 - - - +
28C ALA* 1.3 61.5 + - - +
29C VAL* 3.3 8.3 + - + +
58C TRP* 4.2 19.3 - - + -
59C SER* 4.3 8.1 - - - +
82C TRP* 4.1 24.7 - - + -
149C GLU 2.7 11.0 + - - +
150C ILE* 3.5 5.1 - - + -
151C SER 3.0 21.6 + - - +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PRO 3.3 6.3 + - - +
27C VAL* 1.3 71.1 - - - +
29C VAL* 1.3 62.6 + - - +
30C SER* 4.0 0.9 + - - -
57C THR* 3.7 8.0 - - - +
58C TRP* 3.8 12.3 - - - +
59C SER 4.7 1.2 + - - -
151C SER* 3.5 15.9 - - - +
153C ASP* 5.8 1.8 - - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.9 14.8 - - + +
28C ALA* 1.3 74.6 - - - +
30C SER* 1.3 66.5 + - - +
31C VAL* 4.1 11.0 - - + -
56C THR* 3.8 26.7 - - + -
57C THR 3.4 6.1 - - - +
58C TRP* 4.5 3.1 - - + -
82C TRP* 4.8 0.2 - - + -
84C PRO* 3.9 26.5 - - + -
86C LEU* 4.2 6.1 - - + -
150C ILE* 3.8 23.8 - - + -
151C SER 2.7 11.9 + - - +
152C VAL* 3.1 10.0 - - + -
153C ASP* 2.8 26.2 + - - +
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 4.0 1.1 + - - -
29C VAL* 1.3 72.6 + - - +
31C VAL* 1.3 62.2 + - - +
55C GLN* 3.4 3.1 - - - +
56C THR* 3.3 7.8 - - - +
57C THR* 2.8 56.2 + - - +
153C ASP* 3.1 15.0 + - - +
154C PRO 4.1 6.6 + - - -
155C THR* 4.5 13.1 - - - -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.1 7.4 - - + -
30C SER* 1.3 79.3 - - - +
32C SER* 1.3 68.3 + - - +
33C LEU* 4.7 0.9 - - + -
54C GLN* 4.4 16.8 - - + -
55C GLN 3.4 7.0 - - - +
56C THR* 4.8 0.9 - - - +
86C LEU* 3.6 33.2 - - + -
140C ILE* 4.4 24.0 - - + -
152C VAL* 4.3 19.3 - - + -
153C ASP 2.9 6.8 + - - +
154C PRO* 3.4 21.3 - - - +
155C THR* 4.7 0.9 - - - -
178C GLN* 3.8 3.8 - - - +
195C VAL* 4.9 16.0 - - + +
197C VAL* 6.5 0.7 - - + -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 1.3 78.8 - - - +
33C LEU* 1.3 67.6 + - - +
34C LYS* 3.6 20.8 + - - +
53C TRP 3.6 0.2 - - - +
54C GLN 3.8 0.2 - - - -
55C GLN* 2.9 57.2 + - - +
155C THR* 3.7 14.5 + - - -
178C GLN* 4.2 15.1 + - - +
197C VAL* 6.0 1.1 - - - -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 4.7 2.7 - - + -
32C SER* 1.3 80.7 + - - +
34C LYS* 1.3 65.3 + - - +
35C PHE* 3.7 37.0 + - + -
52C PHE* 3.6 38.1 - - + -
53C TRP 3.6 1.3 - - - -
54C GLN* 3.9 12.3 - - + -
138C ILE* 4.3 15.5 - - + -
140C ILE* 3.8 26.9 - - + -
176C VAL* 5.3 2.9 - - - +
178C GLN* 3.9 11.0 + - - +
197C VAL* 3.9 29.4 - - + -
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B SER* 5.3 11.2 - - - -
187B CYS* 5.8 1.3 - - - -
32C SER* 3.6 21.9 + - - +
33C LEU* 1.3 76.7 - - - +
35C PHE* 1.3 64.4 + - - +
36C ILE* 3.5 3.7 - - - +
52C PHE* 4.1 1.1 - - - -
53C TRP* 2.8 59.3 + - + +
55C GLN* 3.4 29.6 + - - +
114C MET* 4.6 6.7 - - - -
155C THR* 5.6 4.8 - - - +
161C ASP 5.6 1.8 - - - -
164C TYR* 4.0 34.3 - - + -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.0 28.3 - - + -
34C LYS* 1.3 72.0 - - - +
36C ILE* 1.3 64.1 + - - +
37C ASN 5.4 0.2 - - - -
38C ILE* 5.6 0.9 - - + -
50C VAL* 3.5 32.8 - - + -
51C VAL 3.9 1.6 - - - -
52C PHE* 4.1 9.9 - + + -
138C ILE* 4.2 14.4 - - + -
161C ASP 4.4 10.8 + - - +
164C TYR* 3.7 4.7 - - - +
165C PHE* 3.7 22.3 + - + +
173C ILE* 3.7 19.1 - - + -
176C VAL* 4.2 16.8 - - + -
197C VAL* 4.0 22.0 - - + -
199C LEU* 3.9 45.5 - - + -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR 4.7 14.6 - - - +
90B ASN* 6.0 1.1 - - - -
34C LYS 3.5 16.4 - - - +
35C PHE* 1.3 74.3 - - - +
37C ASN* 1.3 65.3 + - + +
51C VAL* 2.8 27.4 + - + +
52C PHE* 3.9 1.1 - - - -
53C TRP* 3.5 45.1 - - + +
116C SER* 5.5 0.2 - - - +
164C TYR* 3.6 36.3 - - + +
165C PHE* 3.6 3.8 - - - -
166C SER* 2.7 33.6 + - - +
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Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 4.7 3.2 - - + +
122B SER* 2.9 38.0 + - - -
35C PHE* 5.4 0.3 - - - -
36C ILE* 1.3 81.3 - - + +
38C ILE* 1.3 82.7 + - - +
39C LEU* 3.6 19.6 - - + +
50C VAL* 3.6 3.3 - - - +
51C VAL* 3.0 39.4 + - + +
165C PHE* 3.6 7.9 - - - -
166C SER* 3.3 17.1 + - - -
169C SER* 3.1 21.4 - - - +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 5.6 0.7 - - + -
37C ASN* 1.3 85.4 + - - +
39C LEU* 1.3 64.2 + - - +
40C GLU 4.8 0.2 - - - +
41C VAL* 3.8 28.7 - - + -
48C VAL* 5.2 1.6 - - + -
49C ASP 3.7 10.1 - - - +
50C VAL* 4.7 11.2 - - + +
165C PHE* 3.6 22.6 - - + -
169C SER* 3.0 22.6 + - - +
170C ARG 4.7 0.7 + - - -
171C PHE* 3.6 20.9 - - + -
173C ILE* 4.7 2.7 - - + -
199C LEU* 3.9 25.6 - - + -
201C PHE* 3.7 32.8 - - + -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 5.1 2.3 - - - +
47B GLU* 3.8 28.1 - - + +
92B ILE* 3.8 26.7 - - + -
122B SER* 5.0 2.2 - - - -
37C ASN* 3.6 34.8 - - + +
38C ILE* 1.3 76.2 - - - +
40C GLU* 1.3 62.4 + - + +
49C ASP* 2.9 15.3 + - + +
51C VAL* 3.9 12.1 - - + -
118C ARG* 3.2 52.5 - - - +
170C ARG* 3.3 17.6 + - - -
171C PHE* 4.8 1.7 - - - -
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 1.3 82.2 - - + +
41C VAL* 1.3 76.9 + - - +
42C ASN* 4.8 12.0 + - - +
47C GLU 4.8 0.2 - - - -
48C VAL* 3.4 2.3 - - - -
49C ASP* 2.7 47.7 + - + +
118C ARG* 5.8 1.7 + - - +
120C ARG* 6.1 0.5 - - - -
170C ARG* 4.1 9.9 - - - +
171C PHE* 5.0 0.7 - - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 3.8 10.1 - - + -
40C GLU* 1.3 90.4 - - - +
42C ASN* 1.3 66.7 + - - +
43C GLU 4.3 0.9 - - - +
47C GLU 3.7 4.3 - - - -
48C VAL* 4.0 6.7 - - + -
125C VAL* 3.2 28.7 - - + -
128C VAL* 4.1 16.6 - - + -
170C ARG* 4.7 1.7 + - - +
171C PHE* 3.5 35.1 - - + -
201C PHE* 3.6 19.1 - - + -
203C LYS* 4.9 6.1 + - - +
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Residues in contact with ASN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 4.8 11.8 + - - +
41C VAL* 1.3 76.5 - - - +
43C GLU* 1.3 57.7 + - - +
44C ILE* 2.8 26.2 + - - +
45C THR* 2.9 36.3 + - - +
46C ASN* 2.8 30.8 + - - -
47C GLU* 3.0 15.7 + - + +
125C VAL* 3.9 3.9 - - - +
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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