Contacts of the helix formed by residues 31 - 50 (chain D) in PDB entry 4UC5
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 SER 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C HIS* 4.1 1.8 - - - -
29D PRO 3.5 2.6 + - - -
30D ILE* 1.3 76.8 - - - +
32D LYS* 1.3 54.2 + - - +
33D GLU* 3.7 13.1 + - - -
34D ALA* 3.1 12.7 + - - +
35D SER* 2.8 36.6 + - - -
133D LEU* 4.2 5.0 - - - +
137D ASN* 2.6 31.9 + - - -
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Residues in contact with LYS 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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4C HIS* 3.8 30.6 - - + +
5C TYR* 5.5 2.1 + - - -
31D SER* 1.3 73.0 - - - +
33D GLU* 1.3 68.5 + - + +
35D SER* 3.2 3.7 + - - -
36D GLY* 3.0 25.1 + - - -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D SER* 3.2 10.0 + - - +
32D LYS* 1.3 87.5 + - + +
34D ALA* 1.3 64.5 + - - +
36D GLY* 3.3 2.4 + - - -
37D LEU* 3.1 22.9 + - - +
136D ASN 4.9 2.8 - - - +
137D ASN* 3.6 30.5 - - - +
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Residues in contact with ALA 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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30D ILE* 3.7 18.4 - - + -
31D SER* 3.1 20.0 + - - +
33D GLU* 1.3 79.0 - - - +
35D SER* 1.3 63.6 + - - +
37D LEU* 3.3 1.9 + - - +
38D VAL* 3.0 28.1 + - - +
133D LEU* 4.2 7.2 - - + -
136D ASN* 3.7 31.6 + - + -
137D ASN* 3.9 7.4 + - - +
158D LEU* 4.7 0.4 - - + -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 3.0 30.0 + - - -
5C TYR* 3.4 26.7 + - - +
7C THR* 3.8 7.8 + - - +
30D ILE* 3.5 22.5 - - - +
31D SER 2.8 14.4 + - - -
32D LYS 3.5 5.4 - - - -
33D GLU 3.2 0.2 - - - -
34D ALA* 1.3 77.6 - - - +
36D GLY* 1.3 57.2 + - - +
38D VAL 3.4 0.2 + - - -
39D HIS* 3.0 31.4 + - - +
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Residues in contact with GLY 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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5C TYR* 3.8 24.9 - - - -
32D LYS 3.0 13.2 + - - -
33D GLU 3.3 3.1 + - - -
34D ALA 3.3 0.4 - - - -
35D SER* 1.3 77.2 - - - +
37D LEU* 1.3 55.5 + - - +
39D HIS* 4.0 0.9 - - - +
40D ARG* 3.1 34.2 + - - +
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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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33D GLU 3.1 16.4 + - - +
34D ALA* 3.8 4.0 - - - +
36D GLY* 1.3 74.3 - - - +
38D VAL* 1.3 59.8 + - - +
40D ARG* 3.4 28.9 - - - +
41D THR* 2.6 47.5 + - - +
82D ARG* 3.8 13.7 - - - +
136D ASN* 3.4 40.8 - - - +
139D GLY* 3.7 25.1 - - - +
141D PRO* 3.8 12.3 - - + -
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Residues in contact with VAL 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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7C THR* 3.7 9.0 - - + -
30D ILE* 4.7 3.4 - - + -
34D ALA 3.0 21.4 + - - +
35D SER 3.9 3.1 - - - +
37D LEU* 1.3 73.6 - - - +
39D HIS* 1.3 65.2 + - - +
42D ARG* 3.0 62.7 + - - +
136D ASN* 3.5 26.5 - - - +
157D ASP 3.7 14.1 - - - +
158D LEU* 4.0 12.1 - - - +
159D ILE 4.0 5.8 - - - +
160D SER* 3.6 10.2 + - - +
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Residues in contact with HIS 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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5C TYR* 3.7 41.8 - + + +
6C PRO* 3.8 29.2 + - + +
7C THR* 4.5 0.4 - - - +
35D SER 3.0 18.4 + - - +
36D GLY 4.0 2.7 - - - +
38D VAL* 1.3 78.6 - - - +
40D ARG* 1.3 69.8 + - + +
42D ARG* 3.6 7.9 - - - +
43D GLN* 3.1 29.6 + - + +
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Residues in contact with ARG 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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36D GLY 3.1 20.9 + - - +
37D LEU* 3.4 30.5 - - - +
39D HIS* 1.3 82.4 - - + +
41D THR* 1.3 62.2 + - - +
43D GLN* 3.1 7.3 + - - +
44D GLU* 2.8 74.3 + - + +
82D ARG* 3.7 14.6 - - - +
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Residues in contact with THR 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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37D LEU* 2.6 30.1 + - - +
40D ARG* 1.3 77.5 - - - +
42D ARG* 1.3 64.2 + - - +
44D GLU* 3.6 9.3 + - - +
45D ILE* 3.0 42.1 + - + +
82D ARG* 4.6 2.9 + - - -
90D LEU* 4.4 11.9 - - + -
92D VAL* 4.1 8.7 - - + -
141D PRO* 3.6 27.7 - - + +
160D SER* 3.7 20.0 - - - -
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Residues in contact with ARG 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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6C PRO 4.6 1.4 + - - -
7C THR* 2.9 42.2 + - - +
10C ILE* 4.3 4.0 - - - +
38D VAL* 3.0 36.5 + - - +
39D HIS* 3.6 7.6 - - - +
41D THR* 1.3 77.8 - - - +
43D GLN* 1.3 62.1 + - - +
45D ILE 3.4 0.3 + - - -
46D SER* 3.0 21.5 + - - -
156D ALA 3.1 20.0 + - - -
157D ASP 3.8 2.0 + - - -
159D ILE 2.8 25.5 + - - -
160D SER* 3.7 22.4 + - - +
182D SER* 3.4 35.6 + - - +
183D CYS* 3.8 4.6 - - - +
184D PRO* 3.8 21.1 - - + +
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Residues in contact with GLN 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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39D HIS* 3.1 19.6 + - + +
40D ARG* 3.1 11.0 + - - +
42D ARG* 1.3 79.5 - - - +
44D GLU* 1.3 63.6 + - + +
46D SER* 3.1 14.2 + - - -
47D ASP* 3.1 38.5 + - - +
52D ARG* 3.9 4.5 + - - -
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Residues in contact with GLU 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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40D ARG* 2.8 62.2 + - + +
41D THR* 3.6 11.4 + - - +
43D GLN* 1.3 73.5 - - + +
45D ILE* 1.3 63.1 + - - +
47D ASP* 3.2 21.7 + - - +
48D LEU* 3.2 17.0 + - - +
53D ASP* 5.1 1.4 - - - +
55D ARG* 3.5 20.6 + - - +
82D ARG* 5.1 0.5 + - - -
90D LEU* 3.5 34.5 - - + +
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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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41D THR* 3.0 31.5 + - + +
42D ARG 3.8 3.4 - - - +
44D GLU* 1.3 70.9 - - - +
46D SER* 1.3 61.7 + - - +
48D LEU* 3.0 10.4 + - + +
49D VAL* 2.8 34.9 + - + +
57D LEU* 3.9 34.8 - - + -
90D LEU* 3.8 16.4 - - + -
92D VAL* 4.5 3.8 - - + -
160D SER 3.6 20.9 - - - +
161D TRP* 3.9 19.1 - - + +
184D PRO* 3.9 18.2 - - + -
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Residues in contact with SER 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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42D ARG 3.0 13.5 + - - -
43D GLN* 3.2 20.0 + - - -
45D ILE* 1.3 74.9 - - - +
47D ASP* 1.3 61.8 + - - -
49D VAL* 3.1 4.9 + - - -
50D HIS* 3.1 30.3 + - - -
52D ARG* 3.4 15.8 + - - -
184D PRO* 4.4 1.2 - - - +
230D ASP* 2.5 41.3 + - - -
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Residues in contact with ASP 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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43D GLN* 3.1 27.4 + - - +
44D GLU* 3.3 15.2 - - - +
45D ILE 3.1 0.2 - - - -
46D SER* 1.3 75.4 - - - +
48D LEU* 1.3 61.3 + - - +
50D HIS 3.6 0.3 + - - -
51D GLY 3.2 2.8 + - - -
52D ARG* 2.8 70.8 + - + +
53D ASP* 3.4 15.8 + - + +
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Residues in contact with LEU 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 GLU 3.4 10.8 - - - +
45D ILE* 3.0 11.9 + - + +
47D ASP* 1.3 75.6 - - - +
49D VAL* 1.3 66.9 + - + +
50D HIS 3.3 0.5 + - - -
51D GLY* 3.3 10.4 + - - -
53D ASP* 3.3 48.5 - - + +
55D ARG* 3.4 18.6 - - + +
57D LEU* 3.8 38.8 - - + +
90D LEU* 4.1 24.9 - - + -
263D LYS* 4.2 9.2 - - - +
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Residues in contact with VAL 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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45D ILE* 2.8 26.2 + - + +
46D SER* 3.1 10.3 + - - +
48D LEU* 1.3 77.7 - - + +
50D HIS* 1.3 76.0 + - + +
184D PRO* 5.1 0.7 - - + -
230D ASP 4.1 13.9 - - - +
231D CYS 4.0 20.2 - - - +
232D HIS* 3.9 28.7 - - + -
261D THR* 2.8 35.9 + - + -
263D LYS* 3.4 15.0 - - - +
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Residues in contact with HIS 50 (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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46D SER* 3.1 27.3 + - - +
49D VAL* 1.3 89.6 + - + +
51D GLY* 1.3 60.8 + - - +
52D ARG* 3.3 33.6 + - - +
229D PRO* 3.0 32.4 + - + +
230D ASP* 3.1 17.7 + - - -
261D THR* 4.7 11.3 - - + -
263D LYS* 4.9 2.2 - - - -
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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