Contacts of the helix formed by residues 31 - 45 (chain B) in PDB entry 4KMH
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 PRO 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LEU 3.6 7.6 - - - +
30B PHE* 1.3 85.3 - - + +
32B PRO* 1.3 67.5 - - + +
33B GLY 3.2 0.7 - - - -
34B LEU* 3.1 27.7 + - + +
35B HIS* 2.9 24.1 + - - +
98B LEU 3.5 17.0 - - - +
99B TYR* 3.6 39.7 - - + -
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Residues in contact with PRO 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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30B PHE 3.6 4.7 - - - +
31B PRO* 1.3 84.7 - - + +
33B GLY* 1.3 57.8 + - - +
35B HIS* 3.4 12.3 + - + +
36B ALA* 3.4 20.3 + - - +
99B TYR 4.3 4.3 - - - +
191B PRO* 3.8 28.8 - - + +
192B PHE* 3.6 31.6 - - + -
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Residues in contact with GLY 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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32B PRO* 1.3 76.2 - - - +
34B LEU* 1.3 63.2 + - - +
35B HIS 3.2 0.8 + - - -
36B ALA* 3.6 7.8 + - - +
37B ILE* 3.4 23.3 + - - +
96B SER* 5.1 0.6 + - - -
97B ASP 3.8 14.6 - - - -
98B LEU* 2.9 22.8 + - - -
190B THR* 4.2 14.2 - - - +
192B PHE* 3.6 5.6 - - - -
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Residues in contact with LEU 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 PHE* 4.2 31.0 - - + -
31B PRO* 3.1 26.8 + - + +
33B GLY* 1.3 75.6 - - - +
35B HIS* 1.3 63.9 + - - +
37B ILE 3.7 0.3 + - - -
38B TYR* 3.2 30.0 + - + +
70B TYR* 3.8 34.5 - - + -
93B PHE* 4.0 19.9 - - + -
98B LEU* 3.7 28.1 + - + +
99B TYR* 5.3 2.2 - - + +
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Residues in contact with HIS 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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23B PRO* 5.4 2.4 - - + +
24B PRO* 3.6 39.5 - - + +
27B ALA* 5.0 13.0 - - + +
30B PHE* 4.2 18.9 - + + +
31B PRO 2.9 13.1 + - - +
32B PRO* 3.4 16.4 - - + +
33B GLY 3.2 0.4 - - - -
34B LEU* 1.3 82.7 - - - +
36B ALA* 1.3 60.6 + - - +
38B TYR* 3.8 5.5 + - - +
39B GLY* 3.2 18.0 + - - -
42B ARG* 5.3 2.5 - - - -
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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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32B PRO 3.4 8.4 + - - +
33B GLY 4.1 0.2 - - - +
34B LEU 3.3 0.8 - - - -
35B HIS* 1.3 78.7 - - - +
37B ILE* 1.3 65.5 + - - +
39B GLY* 3.1 11.2 + - - -
40B GLU 3.4 7.6 + - - -
188B VAL* 4.2 22.7 - - + +
189B GLN 4.6 4.5 - - - +
190B THR* 3.8 33.4 - - + -
191B PRO* 5.7 0.2 - - + -
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Residues in contact with ILE 37 (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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33B GLY 3.4 17.7 + - - +
34B LEU 3.7 1.3 + - - +
35B HIS 3.5 0.2 - - - -
36B ALA* 1.3 74.3 - - + +
38B TYR* 1.3 63.4 + - - +
40B GLU* 3.1 15.0 + - - +
41B CYS* 3.2 12.2 + - - -
91B ILE* 4.3 10.8 - - + -
92B SER 4.6 2.0 - - - +
93B PHE* 3.5 28.0 - - + -
96B SER* 3.5 24.7 - - - +
98B LEU* 4.0 11.4 - - + -
119B GLU* 3.8 17.9 - - + +
188B VAL* 4.7 5.8 - - + -
195B VAL* 4.6 9.9 - - + -
197B PHE* 3.8 34.3 - - + -
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Residues in contact with TYR 38 (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 PRO* 3.9 22.7 - - + +
30B PHE* 4.1 23.3 - + - -
34B LEU* 3.2 22.8 + - + +
35B HIS* 3.9 6.1 - - - +
37B ILE* 1.3 77.1 - - - +
39B GLY* 1.3 57.3 + - - +
41B CYS* 3.2 7.3 + - + +
42B ARG* 2.9 66.8 + - + +
48B GLN 6.1 0.2 - - - -
49B PRO* 2.9 29.2 + - - +
50B ASN* 4.5 2.3 + - - -
51B PRO* 5.4 3.4 - - + -
53B GLN* 6.0 4.5 - - - -
74B TYR* 3.9 22.4 - - - -
93B PHE* 4.1 12.0 - + + -
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Residues in contact with GLY 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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20B PRO* 4.7 10.1 - - - +
35B HIS* 3.2 10.7 + - - -
36B ALA* 3.1 11.3 + - - -
38B TYR* 1.3 79.3 - - - +
40B GLU* 1.3 55.1 + - - +
42B ARG* 3.6 18.5 + - - +
43B ARG* 3.1 24.3 + - - +
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Residues in contact with GLU 40 (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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36B ALA 3.4 3.6 + - - -
37B ILE 3.1 9.9 + - - +
39B GLY* 1.3 74.3 - - - +
41B CYS* 1.3 66.3 + - - +
43B ARG* 2.7 47.4 + - - +
44B LEU* 3.1 24.5 + - + +
185B MET* 4.2 23.3 - - + -
186B GLN* 3.1 45.9 + - - +
188B VAL* 3.5 21.1 - - + +
197B PHE* 4.7 2.5 - - + -
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Residues in contact with CYS 41 (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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37B ILE 3.3 16.4 - - - -
38B TYR* 3.2 12.3 + - - +
40B GLU* 1.3 78.0 - - - +
42B ARG* 1.3 57.5 + - - +
44B LEU* 3.4 4.3 + - - -
45B TYR* 2.9 36.6 + - - +
74B TYR* 3.3 29.6 - - + +
91B ILE* 3.7 40.6 - - - -
93B PHE* 4.4 7.6 - - - -
185B MET* 4.2 7.6 - - - -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 4.3 29.4 + - + +
22B ALA 2.4 30.1 + - - -
23B PRO* 4.0 4.6 - - - +
24B PRO* 3.5 28.5 - - - +
35B HIS* 5.3 2.2 - - - -
38B TYR* 2.9 58.5 + - + +
39B GLY* 3.8 11.5 - - - +
41B CYS* 1.3 74.8 - - - +
43B ARG* 1.3 66.3 + - - +
45B TYR 4.2 7.6 - - - +
46B PRO* 3.2 29.3 - - + +
49B PRO* 6.0 4.3 - - + -
74B TYR* 5.6 0.7 - - - +
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Residues in contact with ARG 43 (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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20B PRO* 4.9 17.6 - - + -
39B GLY 3.1 13.6 + - - +
40B GLU* 2.7 41.4 + - - +
42B ARG* 1.3 80.7 - - - +
44B LEU* 1.3 77.9 + - - +
46B PRO* 3.9 7.4 - - - +
184B GLN 3.3 21.0 + - - -
186B GLN* 4.1 11.3 - - - +
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Residues in contact with LEU 44 (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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40B GLU* 3.1 17.0 + - + +
41B CYS* 3.9 0.4 - - - +
43B ARG* 1.3 106.7 - - - +
45B TYR* 1.3 86.2 + - + +
46B PRO* 3.4 7.7 - - - +
47B ASP* 5.1 0.5 - - - +
89B HIS* 4.4 2.9 - - + -
184B GLN* 3.4 55.3 + - + +
185B MET* 3.6 26.7 - - - -
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Residues in contact with TYR 45 (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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41B CYS 2.9 20.8 + - - +
42B ARG* 3.3 8.7 - - - +
44B LEU* 1.3 98.4 - - + +
46B PRO* 1.3 64.8 - - - +
47B ASP* 3.2 6.4 + - - -
48B GLN* 3.4 38.8 + - + +
49B PRO* 5.0 1.4 - - - +
74B TYR* 3.5 44.3 - + + -
75B ARG 3.9 12.1 - - - -
76B ASN* 2.8 35.5 + - + -
89B HIS* 2.7 39.2 + - + +
91B ILE* 4.7 3.1 - - + -
184B GLN* 3.5 5.9 + - - -
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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
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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