Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 1U2Q
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 CYS 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 1.3 92.1 - - - +
17A ARG* 1.3 62.4 + - + +
19A PRO* 3.0 11.0 - - - +
20A MET* 3.0 31.6 - - - +
55A ASP* 3.5 21.1 - - - -
58A ALA* 4.2 4.9 - - - -
126A ASP* 5.0 2.7 - - - +
127A PRO* 4.6 11.2 - - + -
128A TYR* 3.8 31.0 - - - -
135A PHE* 4.0 18.2 - - + -
164A CL 2.8 10.3 - - + +
165A GOL 5.0 0.2 - - - -
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS* 4.4 9.3 - - + +
12A THR* 4.8 5.7 + - - +
16A CYS* 1.3 76.5 - - - +
18A SER* 1.3 68.4 + - - +
20A MET* 3.1 8.7 + - - +
21A ALA* 3.1 21.0 + - - +
89A LEU* 3.5 20.2 - - + +
90A ASP* 3.5 21.8 + - - +
93A HIS* 3.7 24.3 + - - -
124A VAL* 2.6 55.4 + - + -
125A GLU 3.7 8.7 - - - -
126A ASP* 3.5 39.3 + - - +
127A PRO* 3.9 14.1 - - + -
138A VAL* 4.1 7.4 - - + -
142A ILE* 3.9 5.9 - - - +
164A CL 4.2 2.6 - - - +
165A GOL 5.2 6.3 + - - -
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.4 31.8 - - - +
10A VAL 4.0 0.9 - - - -
11A CYS* 2.9 29.3 + - - -
14A ASN* 2.5 27.7 + - - +
17A ARG* 1.3 75.7 - - - +
19A PRO* 1.3 66.7 - - - +
21A ALA* 3.2 3.7 + - - +
22A GLU* 3.0 29.1 + - - +
42A SER* 3.6 4.6 - - - -
43A ALA 4.1 0.2 + - - -
89A LEU* 3.9 10.2 - - - +
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Residues in contact with PRO 19 (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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11A CYS* 4.4 0.2 - - - -
14A ASN* 3.7 6.3 - - - +
15A ILE* 3.3 10.3 - - - +
16A CYS* 3.0 40.6 - - - +
18A SER* 1.3 100.2 - - - +
20A MET* 1.3 59.1 + - + +
22A GLU* 3.5 2.8 + - + +
23A LYS* 2.9 32.8 + - - +
42A SER* 3.8 9.6 - - - +
54A ALA* 4.4 7.9 - - + -
58A ALA* 5.5 0.4 - - + -
62A LEU* 5.1 2.5 - - + -
71A HIS* 3.6 31.9 - - + +
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS 3.0 24.0 - - - +
17A ARG 3.1 5.0 + - - +
19A PRO* 1.3 75.0 - - + +
21A ALA* 1.3 67.6 + - - +
23A LYS* 3.3 2.4 + - - +
24A MET* 2.9 34.6 + - - +
58A ALA* 4.0 25.6 - - + +
61A VAL* 4.0 24.5 - - + -
62A LEU* 4.1 20.9 - - + -
127A PRO* 6.0 0.4 - - - -
135A PHE* 3.8 33.0 - - + +
138A VAL* 4.4 13.0 - - + -
139A PHE* 4.1 20.6 - - + +
142A ILE* 4.1 7.6 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.4 37.0 - - + -
17A ARG 3.1 9.7 + - - +
18A SER* 3.5 5.8 - - - +
20A MET* 1.3 78.6 - - - +
22A GLU* 1.3 64.8 + - - +
24A MET* 3.8 0.9 - - - +
25A PHE* 2.9 27.9 + - - +
89A LEU* 5.1 1.8 - - + -
110A LEU* 4.9 5.4 - - + -
142A ILE* 4.1 26.4 - - + +
146A LEU* 4.7 0.9 - - - +
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Residues in contact with GLU 22 (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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9A PHE* 3.4 12.7 - - - -
18A SER 3.0 14.0 + - - +
19A PRO* 3.5 5.8 - - - +
21A ALA* 1.3 75.9 - - - +
23A LYS* 1.3 86.8 + - + +
26A ALA* 2.9 31.9 + - + +
40A VAL* 3.6 25.7 - - + +
41A THR* 4.1 16.2 - - - +
42A SER* 2.6 35.4 + - - +
71A HIS* 3.6 13.0 - - - -
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 2.9 17.4 + - - +
20A MET 4.0 1.8 - - - +
22A GLU* 1.3 100.7 + - + +
24A MET* 1.3 61.1 + - - +
26A ALA* 3.6 6.0 - - + +
27A GLN* 2.9 31.2 + - - +
30A ARG* 3.8 4.2 + - - +
62A LEU* 4.4 13.9 - - + -
67A TYR* 4.1 2.8 - - + -
68A PRO* 3.7 34.3 - - + +
69A THR* 5.1 1.3 - - - -
70A ASP 2.7 29.3 + - - +
71A HIS* 3.3 32.2 - - - +
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Residues in contact with MET 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 2.9 31.8 + - - +
21A ALA 3.8 2.5 - - - +
23A LYS* 1.3 75.2 - - - +
25A PHE* 1.3 64.1 + - - +
27A GLN* 3.4 2.6 + - - +
28A GLN* 3.0 31.7 + - - +
62A LEU* 3.9 14.1 - - + -
67A TYR* 3.7 18.9 - - + +
139A PHE* 3.5 61.7 - - + +
142A ILE* 3.6 18.4 - - + -
143A GLU* 3.6 21.1 - - + +
146A LEU* 3.9 10.1 - - + -
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Residues in contact with PHE 25 (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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7A VAL* 4.4 11.2 - - + -
9A PHE* 3.9 20.6 - + + -
21A ALA 2.9 17.8 + - - +
22A GLU 3.8 2.9 - - - +
24A MET* 1.3 74.2 - - - +
26A ALA* 1.3 65.5 + - - +
28A GLN* 3.2 7.6 + - - +
29A LEU* 2.9 43.7 + - + +
38A VAL* 4.9 0.7 - - + -
40A VAL* 3.8 22.9 - - + -
146A LEU* 3.8 16.9 - - + +
149A LEU* 3.5 34.3 - - + -
150A HIS* 3.6 37.0 - + - -
153A VAL* 3.7 24.5 - - + -
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Residues in contact with ALA 26 (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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22A GLU* 2.9 20.9 + - + +
23A LYS* 3.6 8.7 - - + +
25A PHE* 1.3 78.0 - - - +
27A GLN* 1.3 62.1 + - - +
29A LEU* 3.1 6.6 + - - +
30A ARG* 2.9 38.8 + - - +
40A VAL* 4.4 20.6 - - + +
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Residues in contact with GLN 27 (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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23A LYS 2.9 18.6 + - - +
24A MET 3.5 5.6 - - - +
26A ALA* 1.3 76.0 - - - +
28A GLN* 1.3 64.4 + - - +
30A ARG* 2.7 61.1 + - - +
31A HIS* 3.0 40.0 + - + +
66A GLY 3.2 23.6 - - - +
67A TYR* 3.5 21.7 - - + -
68A PRO* 3.4 13.8 - - - +
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Residues in contact with GLN 28 (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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24A MET* 3.0 17.9 + - - +
25A PHE* 3.6 5.4 - - - +
27A GLN* 1.3 75.1 - - - +
29A LEU* 1.3 64.8 + - - +
31A HIS* 2.8 26.1 + - + +
32A ARG* 2.9 19.9 + - + +
67A TYR* 4.4 16.5 + - + +
143A GLU* 5.4 11.1 + - - +
146A LEU* 3.4 31.6 - - - +
147A PRO* 6.0 0.8 - - - +
150A HIS* 2.8 38.6 - - + +
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Residues in contact with LEU 29 (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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25A PHE* 2.9 32.3 + - + +
26A ALA* 3.3 7.6 - - - +
28A GLN* 1.3 75.1 - - - +
30A ARG* 1.3 60.2 + - - +
32A ARG* 3.2 9.6 + - - +
33A GLY 3.2 3.3 + - - -
34A LEU* 2.8 47.3 + - + +
35A GLY* 4.0 4.7 - - - +
38A VAL* 3.5 33.4 - - + +
40A VAL* 3.5 31.9 - - + -
150A HIS* 3.6 27.6 - - + +
153A VAL* 5.0 3.6 - - + -
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Residues in contact with ARG 30 (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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23A LYS* 3.8 3.8 + - - +
26A ALA* 2.9 24.8 + - - +
27A GLN* 2.7 68.1 + - - +
29A LEU* 1.3 73.9 - - - +
31A HIS* 1.3 64.3 + - + +
33A GLY* 3.0 13.9 + - - -
35A GLY* 4.4 16.8 - - - +
68A PRO* 3.7 26.2 - - - +
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Residues in contact with HIS 31 (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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27A GLN* 3.0 50.4 + - + +
28A GLN* 2.8 15.9 + - + +
30A ARG* 1.3 77.0 - - + +
32A ARG* 1.3 61.6 + - + +
33A GLY 3.1 3.9 + - - -
67A TYR* 5.7 1.1 - - - -
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Residues in contact with ARG 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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28A GLN* 2.9 18.7 + - + +
29A LEU* 3.6 5.6 - - - +
30A ARG 3.1 0.2 - - - -
31A HIS* 1.3 79.0 - - + +
33A GLY* 1.3 58.5 + - - +
34A LEU* 3.1 35.8 + - + +
150A HIS* 2.9 50.1 - - - +
153A VAL* 5.3 0.8 - - - +
154A ASP* 2.7 42.6 + - - -
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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
------------------------------------------------------------
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