Contacts of the helix formed by residues 18 - 39 (chain B) in PDB entry 1II7
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 LYS 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.3 7.7 - - - +
15B GLN 3.0 10.4 + - - +
16B PHE* 3.4 15.0 - - + +
17B HIS* 1.3 79.7 - - - +
19B PRO* 1.3 57.7 - - + +
20B GLN* 3.0 13.8 - - + +
21B ARG* 2.7 41.9 + - + +
22B GLU 3.3 3.5 + - - -
301B TYR* 3.4 26.1 + - + +
324B GLU 4.0 11.1 + - - -
325B TYR* 3.4 42.0 - - + -
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Residues in contact with PRO 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 4.3 23.6 - - - +
14B GLU* 3.7 18.3 - - + +
17B HIS 3.7 8.3 - - - +
18B LYS* 1.3 82.4 - - + +
20B GLN* 1.3 63.5 + - + +
22B GLU* 3.1 10.2 + - + +
23B GLU* 3.0 33.9 + - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 2.9 12.8 + - + +
19B PRO* 1.3 84.3 - - + +
21B ARG* 1.3 62.7 + - - +
23B GLU* 3.3 16.6 + - - +
24B GLU* 3.0 37.9 + - - +
271B ARG* 3.4 21.1 + - - +
301B TYR* 3.1 26.3 + - - +
324B GLU* 3.5 20.9 + - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 2.6 54.8 + - + +
18B LYS* 2.7 18.7 + - + +
20B GLN* 1.3 70.3 - - - +
22B GLU* 1.3 65.6 + - - +
24B GLU* 2.7 38.8 + - - +
25B PHE* 2.8 41.4 + - + -
227B GLU* 3.1 32.0 + - - +
228B ARG 3.3 17.6 + - - +
271B ARG* 4.0 11.5 - - - +
273B PHE* 3.3 18.2 - - - -
301B TYR* 3.6 35.2 - - + +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 3.8 35.7 + - - +
13B TYR 3.2 17.8 + - - +
14B GLU* 3.6 28.1 - - - +
18B LYS 3.3 2.4 + - - -
19B PRO* 3.1 14.5 + - - +
21B ARG* 1.3 77.2 - - - +
23B GLU* 1.3 64.4 + - + +
25B PHE* 3.3 5.7 + - - +
26B ALA* 3.2 19.8 + - - +
60B THR* 4.0 10.2 + - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 3.0 21.9 + - + +
20B GLN* 3.5 18.1 - - - +
22B GLU* 1.3 77.5 - - + +
24B GLU* 1.3 57.1 + - + +
26B ALA* 3.2 8.4 + - - +
27B GLU* 2.8 30.4 + - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 3.0 25.8 + - - +
21B ARG* 2.7 42.9 + - - +
23B GLU* 1.3 75.4 - - + +
25B PHE* 1.3 66.0 + - - +
27B GLU* 3.8 8.6 - - + +
28B ALA* 2.9 25.8 + - - +
227B GLU* 3.7 17.5 - - - +
271B ARG* 2.7 41.7 + - - +
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 5.5 2.5 - - - -
9B ILE* 3.4 25.6 - - - +
10B HIS* 4.1 21.1 - + + +
11B LEU* 4.2 6.4 - - - +
13B TYR* 3.6 30.3 - + - +
15B GLN* 3.7 41.7 - - + -
21B ARG* 2.8 37.7 + - - -
22B GLU* 3.3 7.8 + - - +
24B GLU* 1.3 77.4 - - - +
26B ALA* 1.3 63.1 + - - +
28B ALA* 3.5 3.2 + - - +
29B PHE* 3.3 19.6 + - - +
225B SER* 5.6 0.9 - - - -
226B LEU* 5.4 0.9 - - + +
227B GLU* 3.7 34.1 - - + -
228B ARG 3.9 2.9 - - - -
229B TRP* 4.3 14.6 - + - -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.8 17.4 - - + +
12B GLY 6.2 1.1 - - - +
22B GLU* 3.2 11.0 + - + +
23B GLU* 3.2 11.3 + - - +
25B PHE* 1.3 76.0 - - - +
27B GLU* 1.3 60.7 + - - +
29B PHE 3.2 1.9 + - - -
30B LYS* 2.9 24.1 + - - +
63B LYS* 3.8 38.4 - - + -
67B LEU* 3.4 11.4 - - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 2.8 16.8 + - - +
24B GLU* 3.8 11.0 - - + +
26B ALA* 1.3 74.2 - - - +
28B ALA* 1.3 66.2 + - - +
30B LYS* 3.1 28.2 + - - +
31B ASN* 2.8 55.3 + - - +
63B LYS* 5.8 3.2 + - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU 2.9 18.2 + - - +
25B PHE 3.7 4.9 - - - +
26B ALA 3.3 0.2 - - - -
27B GLU* 1.3 78.4 - - - +
29B PHE* 1.3 62.0 + - - +
31B ASN* 3.2 11.7 + - - +
32B ALA* 3.0 19.4 + - - +
226B LEU* 3.6 32.1 - - + +
227B GLU* 4.1 17.0 - - + +
268B ILE* 4.6 9.8 - - + +
270B VAL* 5.3 2.9 - - + -
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.2 10.1 - - + -
9B ILE* 3.6 39.7 - - + -
11B LEU* 4.1 15.3 - - + -
25B PHE 3.3 5.9 + - - +
26B ALA 3.2 8.4 + - - +
28B ALA* 1.3 76.7 - - - +
30B LYS* 1.3 64.8 + - - +
32B ALA* 3.3 1.2 + - - +
33B LEU* 3.0 63.6 + - + +
46B ILE* 3.7 28.9 - - + -
50B LEU* 4.0 14.8 - - + -
64B ALA 5.3 0.2 - - - -
67B LEU* 3.6 27.4 - - + -
68B LEU* 4.1 15.3 - - + -
226B LEU* 3.7 7.7 - - - +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA 2.9 14.0 + - - +
27B GLU* 3.1 32.6 + - - +
29B PHE* 1.3 77.7 - - - +
31B ASN* 1.3 62.7 + - - +
33B LEU* 3.3 3.0 + - - +
34B GLU* 3.0 48.6 + - - +
63B LYS* 5.4 6.1 - - - +
67B LEU* 3.9 21.2 - - + +
70B ILE* 3.9 19.6 - - + +
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU* 2.8 45.7 + - - +
28B ALA* 3.7 9.8 - - - +
30B LYS* 1.3 76.2 - - - +
32B ALA* 1.3 59.2 + - - +
34B GLU* 3.3 17.0 + - - +
35B ILE* 2.9 37.8 + - + +
268B ILE* 4.6 21.7 - - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.7 28.4 - - + +
28B ALA 3.0 16.2 + - - +
29B PHE 3.3 3.1 + - - +
31B ASN* 1.3 76.0 - - - +
33B LEU* 1.3 58.5 + - - +
35B ILE* 3.3 3.5 + - - +
36B ALA* 2.9 27.0 + - - +
226B LEU* 4.0 8.7 - - + -
255B PHE* 3.7 31.3 - - + -
268B ILE* 4.1 5.3 - - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 5.2 3.8 - - + -
29B PHE* 3.0 64.2 + - + +
30B LYS 3.8 2.9 - - - +
32B ALA* 1.3 74.1 - - - +
34B GLU* 1.3 65.6 + - - +
36B ALA* 3.1 6.7 + - + +
37B VAL* 2.9 28.7 + - - +
44B ILE* 4.0 30.9 - - + +
46B ILE* 5.3 0.9 - - + -
67B LEU* 3.4 29.8 - - + +
68B LEU* 4.6 2.5 - - + +
70B ILE* 4.3 14.8 - - + -
71B PRO* 4.1 13.0 - - + -
78B VAL* 5.7 0.9 - - + -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 3.0 50.3 + - - +
31B ASN* 3.7 17.2 - - - +
32B ALA 3.3 0.2 - - - -
33B LEU* 1.3 78.2 - - - +
35B ILE* 1.3 61.6 + - + +
37B VAL* 3.2 9.7 + - + +
38B GLN* 3.0 33.6 + - + +
70B ILE* 4.2 17.7 - - + +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 2.9 25.4 + - + +
32B ALA 3.6 4.5 - - - +
33B LEU 3.2 0.2 - - - -
34B GLU* 1.3 77.4 - - + +
36B ALA* 1.3 62.5 + - - +
38B GLN* 3.4 16.9 + - - +
39B GLU* 2.9 45.8 + - + +
255B PHE* 3.9 13.9 - - + -
266B VAL* 4.2 20.0 - - + -
267B GLU 5.4 0.7 - - - +
268B ILE* 4.1 29.6 - - + -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 4.0 25.4 - - + -
6B LEU* 6.0 0.9 - - + -
32B ALA 2.9 13.8 + - - +
33B LEU* 3.1 10.5 + - + +
35B ILE* 1.3 77.7 - - - +
37B VAL* 1.3 65.7 + - - +
39B GLU* 3.4 2.2 + - - -
40B ASN 3.2 12.5 + - - -
41B VAL* 3.3 32.1 + - + +
44B ILE* 4.0 15.0 - - + -
76B ILE* 4.5 0.4 - - - +
255B PHE* 4.7 1.1 - - + -
257B ILE* 4.7 3.6 - - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 2.9 18.1 + - - +
34B GLU* 3.5 9.2 - - - +
36B ALA* 1.3 77.6 - - + +
38B GLN* 1.3 58.0 + - + +
40B ASN* 2.7 27.9 + - - +
70B ILE* 3.8 24.7 - - + +
71B PRO* 4.6 4.5 - - + -
74B HIS* 3.5 43.7 - - + +
76B ILE* 4.0 18.9 - - + +
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 3.0 16.7 + - + +
35B ILE* 3.8 22.9 - - + +
37B VAL* 1.3 79.1 - - + +
39B GLU* 1.3 60.5 + - + +
40B ASN* 3.1 3.6 + - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 2.6 60.5 + - - +
35B ILE* 2.9 37.8 + - + +
36B ALA 3.8 5.2 - - - +
37B VAL 3.1 0.4 - - - -
38B GLN* 1.3 77.1 - - + +
40B ASN* 1.3 70.0 + - - +
41B VAL* 4.2 1.3 - - + -
257B ILE* 4.1 18.8 - - + +
264B ARG* 3.1 33.7 + - - -
266B VAL* 5.0 2.4 - - - +
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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