Contacts of the helix formed by residues 5 - 23 (chain i) in PDB entry 5XTD
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 ALA 5 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2i ASN* 3.1 18.7 + - + +
4i LEU* 1.3 79.5 - - - +
6i GLN* 1.3 65.8 + - - +
7i PRO 3.4 0.4 - - - -
8i VAL* 3.1 18.9 + - - +
9i ILE* 3.3 14.6 + - + +
104j TYR* 4.4 13.5 - - + +
165m TYR* 5.4 11.7 - - + -
169m GLU* 3.1 28.3 - - + +
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Residues in contact with GLN 6 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1i MET 4.7 11.7 + - - +
2i ASN 3.4 14.0 + - - +
3i PRO* 3.8 16.1 - - - +
4i LEU 3.3 0.2 - - - -
5i ALA* 1.3 77.1 - - - +
7i PRO* 1.3 72.1 - - + +
9i ILE* 3.1 9.3 + - - +
10i TYR* 2.9 48.9 + - + -
46i LYS* 3.7 26.1 - - - +
169m GLU* 4.9 1.1 + - - +
40w MET* 4.5 12.1 - - - +
292w TYR* 5.7 2.0 + - - -
293w HIS* 5.1 7.9 - - - -
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Residues in contact with PRO 7 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3i PRO 3.5 8.3 - - - +
4i LEU* 3.3 17.0 - - - +
6i GLN* 1.3 92.7 - - + +
8i VAL* 1.3 64.0 + - + +
10i TYR* 4.2 5.8 - - + +
11i SER* 2.9 28.8 + - - -
40w MET* 6.2 2.5 - - + -
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Residues in contact with VAL 8 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4i LEU 4.6 9.9 - - - +
5i ALA* 3.1 11.4 + - - +
6i GLN 3.1 0.8 - - - -
7i PRO* 1.3 80.0 - - + +
9i ILE* 1.3 58.6 + - + +
11i SER* 3.1 9.5 + - - -
12i THR* 3.1 22.7 - - - +
158m TRP* 4.2 21.5 - - + -
161m PHE* 4.3 1.8 - - + -
162m VAL* 4.3 7.9 - - + -
165m TYR* 3.3 44.6 - - + +
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Residues in contact with ILE 9 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5i ALA* 3.3 9.1 + - + +
6i GLN* 3.1 9.7 + - - +
8i VAL* 1.3 79.3 - - + +
10i TYR* 1.3 65.5 + - + +
12i THR* 2.3 36.3 + - - +
13i ILE* 2.9 8.3 + - + +
39i ALA* 3.4 25.6 - - + +
42i PRO* 4.0 17.9 - - + -
43i VAL* 4.4 17.0 - - + -
162m VAL* 4.8 13.2 - - + -
165m TYR* 5.3 7.0 - - + -
166m ILE* 4.9 4.9 - - + -
169m GLU* 3.3 32.8 - - - +
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Residues in contact with TYR 10 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6i GLN* 2.9 46.1 + - + +
7i PRO* 4.2 4.7 - - + +
9i ILE* 1.3 80.1 - - + +
11i SER* 1.3 63.1 + - - +
13i ILE* 3.2 16.0 + - + +
14i PHE* 3.0 21.7 + - - +
43i VAL* 3.9 20.5 - - + +
46i LYS* 3.0 27.9 + - - -
125i THR* 5.3 7.6 - - - +
129i LEU* 3.9 28.0 - - + +
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Residues in contact with SER 11 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7i PRO 2.9 19.4 + - - -
8i VAL* 3.1 11.4 + - - -
10i TYR* 1.3 78.9 - - - +
12i THR* 1.3 58.1 + - - +
14i PHE* 3.2 9.1 + - - +
15i ALA* 2.9 28.2 + - - +
158m TRP* 4.0 13.2 - - - -
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Residues in contact with THR 12 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8i VAL 3.1 16.6 - - - +
9i ILE* 2.3 29.6 + - - -
11i SER* 1.3 75.1 + - - +
13i ILE* 1.3 60.0 + - - +
15i ALA* 3.9 3.5 - - - +
16i GLY* 2.9 24.8 + - - -
35i MET* 4.4 13.7 - - - +
36i ASN* 4.1 0.5 - - - +
39i ALA* 3.2 19.8 - - - +
158m TRP* 3.0 35.9 - - + +
162m VAL* 3.4 21.6 - - + +
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Residues in contact with ILE 13 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9i ILE* 2.9 13.0 + - + +
10i TYR* 3.6 27.4 - - + +
12i THR* 1.3 76.1 + - - +
14i PHE* 1.3 64.3 + - - +
17i THR* 3.0 9.9 + - - -
36i ASN* 2.8 28.1 - - - +
39i ALA* 3.7 24.2 - - + +
40i PHE* 4.0 37.2 - - + +
43i VAL* 4.6 3.4 - - + -
129i LEU* 4.8 7.4 - - + -
133i TRP* 3.2 32.5 + - + +
134i GLN* 4.5 4.3 - - - +
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Residues in contact with PHE 14 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10i TYR 3.0 12.0 + - - +
11i SER* 3.4 12.1 - - - +
12i THR 3.2 0.2 - - - -
13i ILE* 1.3 77.5 - - - +
15i ALA* 1.3 63.7 + - + +
17i THR* 3.0 5.4 + - - -
18i LEU* 2.9 51.8 + - + +
133i TRP* 4.3 27.1 - + - -
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Residues in contact with ALA 15 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11i SER 2.9 15.6 + - - +
12i THR* 4.4 5.2 - - - +
14i PHE* 1.3 81.8 - - + +
16i GLY* 1.3 57.6 + - - +
18i LEU* 4.1 11.2 - - + -
19i ILE* 2.9 47.1 + - + +
35i MET* 4.6 3.8 - - + -
158m TRP* 5.5 7.0 - - + +
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Residues in contact with GLY 16 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12i THR 2.9 17.6 + - - -
14i PHE 3.0 0.8 - - - -
15i ALA* 1.3 78.9 - - - +
17i THR* 1.3 57.2 + - - +
19i ILE 4.3 0.7 - - - -
20i THR* 4.0 2.3 - - - +
32i GLY* 2.8 33.5 - - - +
35i MET* 4.0 19.3 - - - -
36i ASN* 3.0 18.3 + - - -
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Residues in contact with THR 17 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13i ILE 3.0 3.4 + - - -
16i GLY* 1.3 75.7 - - - +
18i LEU* 1.3 64.4 + - - +
19i ILE 3.2 1.8 - - - -
20i THR* 2.9 25.0 + - - -
21i ALA* 3.6 4.5 + - - +
36i ASN* 2.4 26.3 + - - +
133i TRP* 2.9 45.3 + - + -
136i LEU* 4.1 10.8 - - + -
137i ALA* 3.8 29.8 - - + +
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Residues in contact with LEU 18 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4h LEU* 4.9 11.0 - - + -
6h ILE* 4.2 13.7 - - + -
14i PHE* 2.9 41.4 + - + +
15i ALA* 3.8 9.6 - - + +
17i THR* 1.3 78.4 - - - +
19i ILE* 1.3 58.3 + - + +
21i ALA* 3.1 7.2 + - + +
22i LEU* 3.0 61.5 + - + +
133i TRP* 5.4 0.2 - - - -
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Residues in contact with ILE 19 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15i ALA* 2.9 24.2 + - + +
17i THR 3.2 0.4 - - - -
18i LEU* 1.3 76.7 - - + +
20i THR* 1.3 67.7 + - - +
22i LEU* 3.9 17.4 - - + +
23i SER* 3.2 19.2 + - - -
28i PHE* 3.9 29.4 - - + +
31i VAL* 4.9 5.2 - - + -
32i GLY* 4.4 12.1 - - - +
35i MET* 3.5 27.4 - - + -
155m VAL* 4.1 23.1 - - + -
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Residues in contact with THR 20 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16i GLY 4.0 6.3 - - - +
17i THR 2.9 12.3 + - - -
18i LEU 3.2 0.2 - - - -
19i ILE* 1.3 76.8 - - - +
21i ALA* 1.3 70.8 + - - +
23i SER* 2.3 30.3 + - - +
29i THR* 3.6 33.1 - - - +
32i GLY* 3.7 15.5 - - - -
33i LEU* 3.6 18.2 - - + -
137i ALA* 3.8 12.9 - - + +
140i SER* 3.6 18.3 + - - -
141i ILE* 5.0 5.7 - - - +
144i GLN* 4.5 5.6 + - - -
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Residues in contact with ALA 21 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2h PRO 3.9 22.0 - - - +
3h PHE* 3.9 9.7 - - - -
4h LEU* 3.3 37.9 + - + +
17i THR 4.3 5.6 - - - +
18i LEU* 3.1 12.8 + - + +
20i THR* 1.3 86.1 + - - +
22i LEU* 1.3 62.0 + - - +
23i SER 3.3 0.3 + - - -
140i SER* 5.0 6.7 - - - +
144i GLN* 4.7 6.1 - - - +
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Residues in contact with LEU 22 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3h PHE* 4.1 2.8 - - - -
4h LEU* 4.2 7.0 - - + +
6h ILE* 3.4 49.6 - - + +
7h GLN* 2.8 38.9 + - - +
14h ILE* 4.0 31.4 - - + -
18i LEU* 3.0 38.7 + - + +
19i ILE* 3.9 17.0 - - + +
20i THR 3.2 0.2 - - - -
21i ALA* 1.3 79.6 - - - +
23i SER* 1.3 54.0 + - - +
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Residues in contact with SER 23 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3h PHE* 3.0 21.0 - - - -
7h GLN* 4.2 2.7 - - - +
14h ILE* 6.2 0.4 - - - -
15h ASP* 3.9 4.5 - - - -
19i ILE* 3.2 11.4 + - - -
20i THR* 2.3 29.1 + - - +
22i LEU* 1.3 81.2 - - - +
24i SER* 1.3 59.9 + - - +
25i HIS 4.1 0.4 - - - -
28i PHE* 3.5 29.2 - - - -
29i THR* 3.0 22.3 - - - +
86i MET* 4.3 5.1 - - - +
144i GLN* 4.5 1.2 + - - -
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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
------------------------------------------------------------
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