Contacts of the helix formed by residues 11 - 32 (chain A) in PDB entry 3V5Z
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 PHE 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 3.0 3.2 + - - +
10A VAL* 1.3 96.2 - - + +
12A THR* 1.3 61.4 + - - +
13A ALA 3.4 2.2 - - - -
14A PRO* 3.2 5.4 - - - +
15A HIS* 2.9 39.2 + + - +
57A HIS* 5.4 0.2 - + - -
61A GLU* 3.0 39.3 - - + -
65A ILE* 4.1 17.5 - - + -
66A ILE* 4.7 2.2 - - + -
130A GLU* 3.2 50.3 - - + -
131A GLU* 3.7 20.2 - - + -
134A PHE* 3.8 19.7 - + + -
135A GLN* 3.8 20.2 - - + +
138A LEU* 4.2 3.4 - - + -
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Residues in contact with THR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 2.4 34.8 + - - +
11A PHE* 1.3 77.4 - - - +
13A ALA* 1.3 61.0 + - - +
15A HIS* 3.7 3.7 - - - +
16A TRP* 2.8 31.2 + - + +
19A LYS* 5.0 2.0 + - - +
131A GLU* 5.0 12.2 + - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 5.4 1.4 + - - -
12A THR* 1.3 75.2 - - + +
14A PRO* 1.4 75.8 - - + +
16A TRP* 3.2 12.8 + - + +
17A ARG* 3.1 20.8 + - - +
151A LYS* 5.5 7.6 - - - +
155A ILE* 4.2 17.7 - - + -
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Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 5.6 0.7 - - - +
10A VAL 3.7 20.0 - - - +
11A PHE* 3.2 13.2 - - - +
13A ALA* 1.4 95.7 - - + +
15A HIS* 1.3 58.3 + - - +
17A ARG* 3.2 9.0 + - + +
18A MET* 2.9 31.5 + - - +
57A HIS* 3.7 13.9 - - + -
154A VAL* 4.3 7.0 - - + -
155A ILE* 4.6 8.5 - - + -
158A HIS* 3.6 42.6 - - + +
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Residues in contact with HIS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 2.9 32.6 + + + +
12A THR* 3.9 2.9 - - - +
14A PRO* 1.3 76.5 - - - +
16A TRP* 1.3 59.4 + - - +
18A MET* 3.9 4.7 - - + +
19A LYS* 2.9 44.3 + - - +
57A HIS* 3.3 16.1 + + - -
61A GLU* 3.4 2.4 + - - -
127A MET* 3.5 38.5 - - + +
130A GLU* 2.7 20.6 - - + -
131A GLU* 2.7 28.8 + - - +
201A FEO 2.0 27.5 + - - -
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Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 2.8 24.7 + - + +
13A ALA* 3.2 12.5 + - + +
15A HIS* 1.3 72.8 - - - +
17A ARG* 1.3 90.5 + - + +
19A LYS* 3.8 16.2 - - - +
20A GLN* 3.1 59.7 + - + +
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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
----------------------------------------------------------
13A ALA 3.1 12.0 + - - +
14A PRO* 3.2 10.5 + - + +
16A TRP* 1.3 88.5 - - + +
18A MET* 1.3 71.5 + - + +
20A GLN* 3.2 28.8 + - - +
21A LEU* 2.9 50.6 + - + +
24A LEU* 5.4 4.6 - - - +
53A GLU* 3.0 42.8 + - - +
158A HIS* 6.3 0.7 - - + -
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Residues in contact with MET 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 2.9 29.4 + - - +
15A HIS* 3.9 2.5 - - - +
17A ARG* 1.3 92.4 - - + +
19A LYS* 1.3 56.7 + - - +
21A LEU* 3.2 9.0 + - - +
22A VAL* 2.9 31.8 + - - +
53A GLU* 4.2 15.7 - - + +
54A PHE* 3.5 35.9 - - + -
56A MET* 5.2 0.2 - - + -
57A HIS* 3.7 44.6 - - + +
123A PHE* 4.0 6.3 - - + -
127A MET* 3.8 19.1 - - - -
158A HIS* 4.0 14.6 - - + -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 5.0 1.6 + - - +
15A HIS* 2.9 39.2 + - - +
16A TRP* 3.8 20.5 - - - +
18A MET* 1.3 69.5 - - - +
20A GLN* 1.3 60.6 + - - +
22A VAL* 3.6 9.1 - - - +
23A GLY* 2.9 25.8 + - - -
124A LEU* 4.6 11.9 - - + -
127A MET* 4.1 20.6 - - + -
131A GLU* 4.7 9.0 - - - -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.1 53.0 + - + +
17A ARG* 3.2 36.0 + - - +
19A LYS* 1.3 77.2 - - - +
21A LEU* 1.3 57.1 + - - +
23A GLY* 3.3 2.9 + - - -
24A LEU* 3.0 40.1 + - + +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 2.9 47.6 + - + +
18A MET* 3.2 9.4 + - - +
20A GLN* 1.3 73.0 - - - +
22A VAL* 1.3 64.7 + - - +
24A LEU* 3.2 16.3 + - + +
25A TYR* 3.0 28.6 + - - +
50A THR* 3.9 27.8 + - + +
53A GLU* 3.8 37.0 - - + +
54A PHE* 3.9 22.2 - - + -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET 2.9 19.9 + - - +
19A LYS* 3.3 11.2 + - - +
21A LEU* 1.3 74.8 - - - +
23A GLY* 1.3 65.1 + - - +
24A LEU 3.3 0.2 + - - -
25A TYR* 3.4 25.9 + - + +
26A CYS* 3.0 33.0 + - - -
54A PHE* 4.1 2.0 - - + -
120A THR* 4.0 24.7 - - + -
123A PHE* 3.9 24.9 - - + -
124A LEU* 4.8 15.7 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS 2.9 14.6 + - - -
20A GLN* 3.7 4.3 - - - -
21A LEU 3.3 0.2 - - - -
22A VAL* 1.3 77.5 - - - +
24A LEU* 1.3 63.7 + - - +
26A CYS* 3.9 5.0 - - - +
27A ASP* 3.1 25.1 + - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 5.4 3.4 - - - +
20A GLN* 3.0 31.9 + - + +
21A LEU* 3.2 22.3 + - + +
23A GLY* 1.3 78.5 - - - +
25A TYR* 1.3 58.2 + - - +
27A ASP* 3.4 8.9 + - + +
28A LYS* 3.0 36.1 + - + +
50A THR* 6.2 0.4 - - - +
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Residues in contact with TYR 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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21A LEU 3.0 22.9 + - - +
22A VAL* 3.6 26.5 - - + +
24A LEU* 1.3 76.3 - - - +
26A CYS* 1.3 75.9 + - - +
28A LYS* 3.9 7.9 - - + +
29A LEU* 2.8 34.6 + - + +
43A LEU* 4.9 1.3 - - + +
46A SER* 6.3 2.7 - - - -
47A LEU* 3.6 26.6 - - + +
50A THR* 4.1 17.9 - - + +
51A PHE* 3.8 22.7 - + - -
54A PHE* 3.8 10.8 - + - -
116A LEU* 4.1 20.0 - - + -
119A PHE* 3.6 15.1 - - - -
120A THR* 2.5 32.0 + - - -
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Residues in contact with CYS 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 VAL* 3.0 35.8 + - - +
23A GLY* 3.9 6.5 - - - +
25A TYR* 1.3 93.9 - - - +
27A ASP* 1.3 63.1 + - - +
29A LEU* 3.4 9.7 + - - +
30A SER* 3.1 24.6 + - - -
120A THR* 4.7 9.2 - - - -
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Residues in contact with ASP 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 GLY 3.1 18.0 + - - +
24A LEU* 3.6 10.3 - - + +
26A CYS* 1.3 77.9 - - - +
28A LYS* 1.3 64.3 + - + +
30A SER* 3.2 19.2 + - - -
31A LYS* 3.0 55.0 + - - +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.0 25.6 + - + +
25A TYR* 3.9 6.5 - - + +
27A ASP* 1.3 74.0 - - + +
29A LEU* 1.3 63.4 + - - +
31A LYS* 3.1 6.7 + - - +
32A THR* 2.6 35.3 + - - +
42A ALA* 5.0 3.2 + - - +
43A LEU* 3.9 16.4 - - + -
46A SER* 2.5 38.2 + - - +
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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 TYR* 2.8 22.1 + - + +
26A CYS* 3.4 11.4 - - - +
28A LYS* 1.3 80.2 - - - +
30A SER* 1.3 62.0 + - - +
32A THR* 3.2 16.7 + - - +
34A PHE* 3.9 21.2 - - + -
43A LEU* 3.5 27.7 - - + +
47A LEU* 5.7 0.2 - - + -
112A LEU* 4.4 4.9 - - + -
113A LYS* 4.4 27.1 - - + +
116A LEU* 3.7 39.7 - - + -
117A GLU* 6.0 3.8 - - + -
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Residues in contact with SER 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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26A CYS 3.1 11.3 + - - -
27A ASP* 3.2 17.0 + - - -
29A LEU* 1.3 78.4 - - - +
31A LYS* 1.3 62.5 + - - +
32A THR 3.4 1.8 - - - +
113A LYS* 6.3 1.1 - - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.0 47.5 + - - +
28A LYS* 3.1 6.3 + - - +
30A SER* 1.3 80.8 - - - +
32A THR* 1.3 63.6 + - - +
33A ASN* 3.6 2.9 + - - +
39A ASP* 4.4 3.1 - - - +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 2.6 25.9 + - - +
29A LEU 3.2 11.1 + - - +
30A SER 4.8 1.7 - - - +
31A LYS* 1.3 78.6 - - - +
33A ASN* 1.3 73.2 + - - +
34A PHE* 3.6 27.2 + - + -
39A ASP* 4.0 23.1 + - - +
40A PHE* 4.6 0.7 - - - +
43A LEU* 3.7 33.5 - - + +
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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