Contacts of the helix formed by residues 34 - 50 (chain B) in PDB entry 7KHE
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 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 2.6 36.8 + - - -
32B GLU 3.2 1.0 + - - -
33B ARG* 1.3 70.8 - - - +
35B PHE* 1.3 65.8 + - - +
36B GLY 3.2 3.2 + - - -
37B HIS* 3.5 9.1 + - - +
38B THR* 3.6 1.2 + - - -
199B ASP* 4.1 7.9 + - - -
1081C PRO* 5.7 6.8 - - - +
1083C GLU* 5.5 4.9 - - - -
1084C ASP* 5.7 4.5 - - - -
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 5.2 3.6 - - + -
46A ILE* 3.5 30.3 - - + -
49A SER* 3.9 16.2 - - - -
50A SER* 3.6 17.7 - - - -
223A ILE* 4.3 6.1 - - + -
227A GLN* 3.7 37.0 - - + -
8B PHE* 3.7 17.9 - + - -
31B LEU* 4.4 12.3 - - + -
32B GLU* 3.1 30.6 + - + +
33B ARG 3.7 10.1 - - - -
34B GLY* 1.3 77.6 - - - +
36B GLY* 1.3 69.1 + - - +
37B HIS 3.3 0.2 - - - -
38B THR* 3.2 11.7 - - + +
39B LEU* 3.0 31.2 + - + +
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.5 10.2 - - - +
34B GLY 3.2 0.6 - - - -
35B PHE* 1.3 76.6 - - - +
37B HIS* 1.3 55.6 + - - +
39B LEU* 4.3 0.7 - - - +
40B GLY* 2.9 25.6 + - - -
187B VAL* 3.9 17.2 - - - +
199B ASP* 3.0 27.7 + - - -
200B LYS 5.8 0.2 - - - -
201B LEU* 3.8 14.0 - - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.7 23.3 - - - +
34B GLY* 3.5 8.4 + - - -
35B PHE 3.3 0.4 - - - -
36B GLY* 1.3 75.5 - - - +
38B THR* 1.3 67.0 + - - +
41B ASN* 2.8 27.9 + - - +
185B TYR* 3.7 27.5 + + - +
187B VAL* 3.7 34.3 - - + +
199B ASP* 5.4 0.7 - - - -
1084C ASP* 5.3 5.4 + - - -
1216C ARG* 4.1 45.2 + - + +
1217C THR* 5.7 0.2 - - - +
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.8 27.7 + - - +
45A ARG* 3.6 28.6 - - - +
46A ILE* 4.6 8.8 - - + +
224A LEU* 5.7 1.6 - - + +
34B GLY 3.6 3.4 + - - -
35B PHE* 3.2 33.8 + - + +
37B HIS* 1.3 76.8 - - - +
39B LEU* 1.3 78.4 + - + +
41B ASN* 4.1 2.2 - - - +
42B ALA* 3.0 31.2 + - - +
1216C ARG 5.5 0.2 - - - -
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Residues in contact with LEU 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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46A ILE* 6.3 0.2 - - + -
224A LEU* 4.0 26.5 - - + -
227A GLN* 4.3 29.8 - - + +
228A LEU* 5.1 9.0 - - + +
231A PHE* 5.3 15.3 - - + -
28B LEU* 5.7 1.8 - - + -
31B LEU* 4.3 20.6 - - + -
35B PHE* 3.0 19.5 + - + +
36B GLY 4.3 0.9 - - - +
38B THR* 1.3 94.5 - - + +
40B GLY* 1.3 66.3 + - - +
42B ALA* 4.5 4.0 - - + -
43B LEU* 2.9 36.6 + - + +
201B LEU* 4.7 11.9 - - + -
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Residues in contact with GLY 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 GLY 2.9 18.4 + - - -
39B LEU* 1.3 77.0 - - - +
41B ASN* 1.3 55.7 + - - +
43B LEU* 3.7 3.8 - - - +
44B ARG* 2.9 30.0 + - - +
185B TYR* 3.7 32.4 - - - +
201B LEU* 4.4 8.4 - - - +
203B ILE* 4.7 3.8 - - - +
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Residues in contact with ASN 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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38A THR* 6.4 0.2 - - - -
41A ASN* 3.6 9.3 - - - +
37B HIS 2.8 22.6 + - - +
38B THR* 4.1 2.0 - - - +
40B GLY* 1.3 70.4 - - - +
42B ALA* 1.3 68.3 + - - +
44B ARG* 3.4 29.2 + - - +
45B ARG* 2.9 34.7 + - - +
185B TYR* 4.0 9.9 - - - +
1216C ARG 4.0 1.5 + - - +
1217C THR* 2.3 47.9 + - - +
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Residues in contact with ALA 42 (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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38A THR* 3.9 25.1 - - + +
42A ALA* 5.3 9.6 - - + -
224A LEU* 6.0 2.7 - - + -
228A LEU* 6.3 0.2 - - + -
38B THR 3.0 20.5 + - - +
39B LEU* 4.0 7.0 - - + +
41B ASN* 1.3 76.2 - - - +
43B LEU* 1.3 65.6 + - + +
45B ARG* 3.9 0.5 - - - +
46B ILE* 3.0 31.7 + - - +
224B LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.1 21.3 - - + -
231A PHE* 3.6 37.7 - - + -
39B LEU* 2.9 31.5 + - + +
40B GLY* 3.7 4.3 - - - +
42B ALA* 1.3 80.5 - - + +
44B ARG* 1.3 64.3 + - - +
46B ILE* 4.2 2.4 - - - +
47B LEU* 2.8 35.8 + - + +
183B ILE* 5.1 7.2 - - + -
201B LEU* 6.5 0.7 - - + -
203B ILE* 5.4 6.5 - - + -
217B ILE* 4.4 7.6 - - + +
220B ALA* 4.2 24.2 - - + -
221B ALA* 4.3 8.3 - - - +
224B LEU* 5.0 3.8 - - + -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY 2.9 22.9 + - - +
41B ASN* 3.2 27.2 + - - +
43B LEU* 1.3 72.3 - - - +
45B ARG* 1.3 73.4 + - - +
47B LEU* 3.7 3.9 - - - +
48B LEU* 2.9 39.0 + - + +
183B ILE* 3.8 42.3 - - + +
184B ALA* 5.3 1.3 - - - +
185B TYR* 3.2 40.3 + - + -
1217C THR* 4.7 3.8 - - - +
1219C GLU* 3.8 11.3 + - - +
534D GLU* 5.7 1.1 - - - -
538D ARG* 2.9 52.7 + - - +
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Residues in contact with ARG 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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34A GLY* 2.6 38.6 + - - +
37A HIS* 3.8 35.3 - - - +
38A THR* 3.3 23.7 + - + +
41B ASN* 2.9 34.2 + - - +
42B ALA 3.9 2.5 - - - +
44B ARG* 1.3 80.7 - - - +
46B ILE* 1.3 53.7 + - - +
48B LEU* 4.9 2.0 - - - -
49B SER* 2.3 48.9 + - - +
1217C THR 5.9 0.8 + - - -
1219C GLU* 6.1 3.2 - - - +
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Residues in contact with ILE 46 (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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35A PHE* 3.7 34.8 - - + -
38A THR* 3.8 17.7 - - + +
42B ALA 3.0 16.9 + - - +
43B LEU* 4.2 2.2 - - - +
45B ARG* 1.3 74.4 - - - +
47B LEU* 1.3 64.8 + - - +
49B SER* 4.2 2.5 - - - -
50B SER 3.0 30.8 + - - +
51B MET* 5.0 0.4 - - + -
220B ALA* 4.5 7.4 - - + +
223B ILE* 3.7 33.7 - - + -
224B LEU* 3.5 45.3 - - + -
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Residues in contact with LEU 47 (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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43B LEU* 2.8 24.2 + - + +
44B ARG 3.7 0.7 - - - +
46B ILE* 1.3 79.6 - - - +
48B LEU* 1.3 59.8 + - - +
51B MET* 3.3 34.7 - - + +
180B VAL* 3.4 40.5 - - + +
183B ILE* 3.6 44.0 - - + -
205B MET* 3.7 21.3 - - + -
216B ALA* 4.5 7.0 - - + +
217B ILE* 4.5 7.0 - - + +
220B ALA* 4.3 18.3 - - + +
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Residues in contact with LEU 48 (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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44B ARG* 2.9 29.4 + - + +
45B ARG* 4.1 2.5 - - - +
47B LEU* 1.3 73.9 - - - +
49B SER* 1.3 64.4 + - - +
151B GLY* 4.4 2.1 - - - -
152B TYR* 5.2 5.7 + - + +
178B SER* 2.9 25.5 + - - -
180B VAL* 4.0 13.7 - - + +
181B GLU 6.2 0.2 - - - +
182B ARG* 6.3 1.3 - - - -
183B ILE* 4.4 20.6 - - + +
534D GLU* 5.6 3.1 - - - +
535D ARG* 3.9 43.1 - - + +
538D ARG* 4.7 13.0 - - + -
539D SER* 4.0 24.5 - - - +
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Residues in contact with SER 49 (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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34A GLY* 5.4 6.6 + - - -
35A PHE* 6.1 0.2 - - - -
45B ARG* 2.3 41.3 + - - +
46B ILE* 4.2 1.4 - - - -
48B LEU* 1.3 86.1 - - - +
50B SER* 1.3 65.9 + - - +
150B ARG* 4.2 1.2 - - - +
151B GLY* 2.9 22.5 - - - -
152B TYR* 4.4 2.3 + - - +
539D SER* 4.9 9.6 - - - -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.6 10.9 - - - -
32A GLU* 5.9 0.3 - - - +
33A ARG 4.2 11.6 + - - -
34A GLY* 5.3 2.3 - - - -
35A PHE* 3.9 31.5 - - - -
46B ILE 3.0 21.0 + - - +
48B LEU 3.5 0.2 - - - -
49B SER* 1.3 83.4 + - - +
51B MET* 1.3 64.4 + - - +
52B PRO* 4.4 1.9 - - - +
150B ARG* 4.5 14.6 - - - -
151B GLY 4.5 1.8 - - - +
223B ILE* 3.9 12.8 - - - +
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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
------------------------------------------------------------
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