Contacts of the helix formed by residues 31 - 46 (chain H) in PDB entry 1W4R
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 GLY 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ARG* 3.3 22.3 - - - -
42G ARG* 4.3 2.8 - - - +
29H PHE* 3.4 4.4 + - - +
30H SER* 1.3 77.2 - - - +
32H LYS* 1.3 65.9 + - - +
33H SER 3.2 2.9 - - - -
34H THR* 3.1 9.7 + - - -
35H GLU* 3.0 19.2 + - - +
149H LEU* 4.1 0.4 - - - -
300H TTP 3.2 11.7 + - - -
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Residues in contact with LYS 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 3.9 9.0 - - + +
25H LEU 3.7 11.4 - - - +
26H GLY* 3.5 21.3 - - - +
27H PRO 2.9 18.8 + - - -
28H MET* 4.0 0.6 - - - +
30H SER* 3.3 12.0 - - - +
31H GLY* 1.3 75.8 - - - +
33H SER* 1.3 57.5 + - - +
35H GLU* 3.3 2.8 + - - +
36H LEU* 2.9 27.7 + - - +
122H ALA* 3.8 16.5 - - + +
123H ALA 3.3 32.3 - - - +
124H LEU* 3.6 2.1 - - - +
149H LEU* 3.7 13.0 - - + -
300H TTP 2.8 67.0 + - - +
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Residues in contact with SER 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LYS* 1.3 73.9 - - - +
34H THR* 1.3 56.2 + - - +
36H LEU* 3.3 9.1 + - - +
37H MET* 3.0 33.2 + - - +
97H ASP* 2.7 21.6 + - - -
300H TTP 2.3 55.1 + - - -
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Residues in contact with THR 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G THR* 3.8 24.6 - - + +
38G ARG* 3.9 25.7 - - + -
41G ARG* 4.1 20.6 + - - +
31H GLY* 3.1 14.5 + - - -
33H SER* 1.3 79.8 - - - +
35H GLU* 1.3 57.2 + - - +
37H MET* 3.3 6.3 + - - +
38H ARG* 2.8 27.7 + - - +
41H ARG* 6.0 0.4 - - - +
300H TTP 5.1 0.7 + - - -
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G GLU* 3.7 14.6 - - - +
38G ARG* 4.2 7.3 - - - +
24H ILE* 3.9 13.9 - - + -
31H GLY 3.0 12.1 + - - +
32H LYS 3.7 6.7 - - - +
34H THR* 1.3 74.7 - - - +
36H LEU* 1.3 64.4 + - - +
38H ARG* 2.9 40.7 + - - +
39H ARG* 2.8 59.3 + - - +
149H LEU* 4.2 19.3 - - + -
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 3.8 9.5 - - + +
32H LYS 2.9 13.6 + - - +
33H SER* 3.4 10.1 - - - +
35H GLU* 1.3 75.6 - - - +
37H MET* 1.3 64.3 + - + +
39H ARG* 3.2 4.7 + - - +
40H VAL* 3.0 35.7 + - + +
52H VAL* 4.5 10.1 - - + -
95H GLY* 3.8 13.7 - - - -
96H ILE 3.7 27.8 - - - +
97H ASP* 3.9 18.8 - - + +
120H ILE* 3.3 42.8 - - + +
121H VAL 4.5 0.9 - - - +
122H ALA* 4.2 8.5 - - + +
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Residues in contact with MET 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H SER* 3.0 21.9 + - - +
34H THR* 3.7 5.6 - - + +
36H LEU* 1.3 82.3 - - + +
38H ARG* 1.3 66.9 + - - +
40H VAL* 4.4 9.2 - - + +
41H ARG* 2.9 73.4 + - + +
44H GLN* 5.9 1.1 - - - +
52H VAL* 3.8 39.5 - - + -
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Residues in contact with ARG 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G SER 2.8 27.5 + - - -
31G GLY* 3.3 36.1 - - - +
34G THR* 3.7 14.8 - - + -
35G GLU* 4.2 17.4 + - - +
149G LEU* 3.8 27.0 - - - +
150G THR 4.4 1.0 + - - +
34H THR 2.8 14.4 + - - +
35H GLU* 2.9 46.6 + - - +
37H MET* 1.3 76.4 - - - +
39H ARG* 1.3 72.4 + - - +
41H ARG* 4.0 7.1 - - - +
42H ARG* 3.2 43.0 + - - +
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Residues in contact with ARG 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 2.9 44.1 + - - +
23H VAL 4.9 1.4 + - - -
24H ILE* 3.7 16.9 - - - +
35H GLU* 2.8 39.9 + - - +
36H LEU 3.6 6.5 - - - +
38H ARG* 1.3 81.6 - - - +
40H VAL* 1.3 67.0 + - - +
42H ARG* 3.3 28.0 + - - +
43H PHE* 3.2 21.8 - - - -
120H ILE* 3.8 20.4 - - + -
145H SER* 4.3 7.5 + - - -
147H VAL* 3.7 35.6 - - - +
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 3.0 38.7 + - + +
37H MET* 4.0 12.3 - - + +
39H ARG* 1.3 77.7 - - - +
41H ARG* 1.3 58.7 + - + +
43H PHE* 3.0 13.6 + - - +
44H GLN* 3.0 24.9 + - + +
50H CYS* 3.8 28.7 - - + -
51H LEU 5.5 0.7 - - - +
52H VAL* 4.4 17.5 - - + -
93H VAL* 4.5 7.9 - - + -
95H GLY* 4.3 14.4 - - - +
120H ILE* 4.3 10.8 - - + -
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Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G THR* 4.1 22.8 + - - +
34H THR* 6.0 0.6 - - - +
37H MET* 2.9 70.7 + - + +
38H ARG* 4.0 7.2 - - - +
40H VAL* 1.3 76.2 - - + +
42H ARG* 1.3 57.8 + - - +
44H GLN* 3.7 21.6 - - - +
45H ILE* 2.9 33.2 + - - +
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Residues in contact with ARG 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G PHE 3.7 20.4 - - - +
30G SER 3.8 6.5 - - - +
31G GLY* 5.4 0.7 - - - -
150G THR* 2.8 37.8 + - - +
151G ALA* 4.0 11.6 + - - +
152G VAL* 3.7 30.1 + - + +
159G GLU* 4.6 9.9 + - - +
22H GLN* 5.8 2.2 + - - +
38H ARG* 3.2 42.8 + - - +
39H ARG* 3.4 32.8 + - - +
40H VAL 3.2 0.4 - - - -
41H ARG* 1.3 77.6 - - - +
43H PHE* 1.3 76.3 + - - +
45H ILE* 3.4 19.6 - - - +
46H ALA* 3.6 3.6 + - - +
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Residues in contact with PHE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL* 3.9 19.5 - - + -
157G PHE 5.8 1.8 - - - -
20H GLN* 6.0 1.6 - - - -
22H GLN* 5.1 7.0 - - - -
39H ARG 3.2 24.2 - - - -
40H VAL 3.0 6.9 + - - +
42H ARG* 1.3 92.4 - - - +
44H GLN* 1.3 64.9 + - - +
46H ALA* 3.1 12.4 + - - -
47H GLN 3.4 0.3 + - - -
48H TYR* 3.1 51.3 + + + +
50H CYS* 4.2 1.8 - - - -
93H VAL* 3.7 35.4 - - + -
118H THR* 4.2 21.3 - - + -
120H ILE* 4.3 16.4 - - + -
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Residues in contact with GLN 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H MET* 5.9 1.0 - - - +
40H VAL* 3.0 15.7 + - + +
41H ARG* 3.3 26.3 + - - +
43H PHE* 1.3 75.6 - - - +
45H ILE* 1.3 58.4 + - - +
47H GLN* 2.9 24.8 + - - -
48H TYR 3.8 14.9 - - - +
50H CYS* 3.8 13.8 - - + -
74H GLU* 4.0 24.7 + - - +
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Residues in contact with ILE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PHE* 4.0 34.5 - - + +
154G MET* 3.9 28.6 - - + +
178G ALA* 4.9 11.1 - - + +
41H ARG 2.9 20.5 + - - +
42H ARG* 3.4 17.0 - - - +
44H GLN* 1.3 77.1 - - - +
46H ALA* 1.3 56.6 + - - +
47H GLN* 3.2 18.1 + - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL* 3.7 31.9 - - + +
153G CYS 4.6 0.2 - - - +
154G MET* 4.4 19.5 - - + +
157G PHE* 3.5 27.4 - - + -
42H ARG 3.6 4.9 + - - +
43H PHE 3.1 9.0 + - - +
45H ILE* 1.3 76.8 - - + +
47H GLN* 1.3 70.3 + - - +
48H TYR* 3.3 8.1 + - + -
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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
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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