Contacts of the helix formed by residues 34 - 51 (chain A) in PDB entry 7KHC
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU 3.4 0.2 + - - -
33A ARG* 1.3 90.2 - - - +
35A PHE* 1.3 63.7 + - - +
36A GLY 3.3 2.2 + - - +
37A HIS* 4.7 1.1 - - - -
38A THR* 3.2 4.2 + - - -
199A ASP* 3.9 6.3 + - - -
45B ARG* 2.7 33.3 + - - +
49B SER* 5.3 6.8 + - - -
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 5.3 9.2 - + - -
31A LEU* 4.8 4.5 - - + -
32A GLU* 3.3 34.5 + - + +
33A ARG 3.4 3.8 - - - -
34A GLY* 1.3 78.5 - - - +
36A GLY* 1.3 68.1 + - - +
37A HIS 3.3 0.9 - - - -
38A THR* 3.6 13.9 - - + -
39A LEU* 2.9 41.1 + - + +
46B ILE* 3.9 25.6 - - + -
49B SER* 5.8 0.2 - - - -
50B SER* 3.3 34.8 - - - -
223B ILE* 4.4 15.7 - - + -
224B LEU* 5.5 4.5 - - + -
227B GLN* 3.1 36.1 - - + -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.1 11.2 - - - +
32A GLU 4.0 6.4 + - - -
34A GLY 3.3 4.2 - - - +
35A PHE* 1.3 80.6 - - - +
37A HIS* 1.3 58.3 + - - +
39A LEU* 4.0 0.9 - - - +
40A GLY* 2.9 21.0 + - - -
187A VAL* 3.5 24.9 - - - -
199A ASP* 4.8 10.0 + - - -
201A LEU* 3.6 12.4 - - - +
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Residues in contact with HIS 37 (chain A).
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* 4.3 2.0 + - - -
35A PHE 3.3 0.2 - - - -
36A GLY* 1.3 71.1 - - - +
38A THR* 1.3 67.3 + - - +
40A GLY 4.4 0.4 - - - +
41A ASN* 2.9 27.8 + - - +
185A TYR* 4.0 24.3 + + + +
187A VAL* 3.6 28.4 - - + +
45B ARG* 3.4 34.1 - - - +
1213C TYR* 5.8 8.1 - + - -
1218C GLY* 4.8 12.5 + - - +
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Residues in contact with THR 38 (chain A).
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 3.2 17.5 + - - -
35A PHE* 3.1 18.3 + - + -
37A HIS* 1.3 77.4 - - - +
39A LEU* 1.3 59.2 + - + +
41A ASN* 3.8 3.5 - - - +
42A ALA* 3.0 28.5 + - + +
41B ASN* 6.3 0.7 - - - +
42B ALA* 3.8 39.4 - - + +
45B ARG* 3.2 23.5 - - - +
46B ILE* 4.3 12.1 - - + +
224B LEU* 4.9 8.1 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 4.9 9.2 - - + -
28A LEU* 5.7 3.4 - - + -
31A LEU* 3.3 34.1 - - + -
35A PHE* 2.9 24.6 + - + +
36A GLY 4.2 0.9 - - - +
38A THR* 1.3 74.0 - - + +
40A GLY* 1.3 68.8 + - - +
42A ALA* 4.4 2.5 - - + +
43A LEU* 2.8 47.9 + - + +
201A LEU* 4.3 11.4 - - + -
224A LEU* 5.1 3.6 - - + -
224B LEU* 4.3 13.7 - - + -
227B GLN* 5.1 8.7 - - + -
228B LEU* 3.8 31.2 - - + -
231B PHE* 6.4 0.9 - - + -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 2.9 17.3 + - - -
37A HIS 3.7 1.3 - - - -
39A LEU* 1.3 75.7 - - - +
41A ASN* 1.3 56.1 + - - +
43A LEU* 3.9 2.0 - - - +
44A ARG 2.9 24.6 + - - -
185A TYR* 3.2 39.9 - - - -
201A LEU* 3.9 11.2 - - - +
203A ILE* 5.2 2.2 - - - +
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS 2.9 17.4 + - - +
38A THR* 3.8 3.6 - - - +
40A GLY* 1.3 73.5 - - - +
42A ALA* 1.3 66.5 + - - +
44A ARG* 3.3 9.4 + - - +
45A ARG* 2.9 29.3 + - - +
185A TYR* 3.5 17.3 + - - +
38B THR* 6.1 0.9 - - - +
41B ASN* 3.0 12.6 - - - +
1087C TYR* 5.3 2.1 + - - -
1215C GLY 3.9 12.5 - - - +
1216C ARG 3.3 6.6 + - - -
1217C THR 2.7 39.7 + - - +
1218C GLY* 3.2 9.2 - - - +
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Residues in contact with ALA 42 (chain A).
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* 3.0 18.0 + - + +
39A LEU* 4.0 4.0 - - + +
41A ASN* 1.3 76.0 - - - +
43A LEU* 1.3 66.3 + - + +
45A ARG* 3.1 2.9 + - - +
46A ILE* 3.0 30.4 + - + +
224A LEU* 4.4 26.5 - - + -
38B THR* 3.7 20.2 - - - +
39B LEU* 6.3 0.2 - - + -
42B ALA* 5.2 11.7 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 2.8 57.1 + - + +
40A GLY 3.9 2.0 - - - +
42A ALA* 1.3 75.9 - - + +
44A ARG* 1.3 62.3 + - - +
46A ILE* 3.9 3.8 - - + +
47A LEU* 2.9 38.3 + - + +
201A LEU* 5.8 1.3 - - + -
203A ILE* 4.3 13.7 - - + -
217A ILE* 3.7 28.5 - - + +
220A ALA* 3.8 22.7 - - + -
221A ALA* 4.4 12.1 - - + +
224A LEU* 5.0 4.7 - - + -
228B LEU* 4.9 9.2 - - + -
231B PHE* 6.2 4.0 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 2.9 18.9 + - - +
41A ASN* 3.6 9.3 + - - +
43A LEU* 1.3 74.6 - - - +
45A ARG* 1.3 65.9 + - - +
47A LEU* 3.5 2.1 - - - +
48A LEU* 3.0 50.4 + - + +
183A ILE* 3.5 44.0 + - + +
184A ALA* 5.2 0.2 - - - +
185A TYR* 3.9 21.8 - - + -
203A ILE* 5.8 0.6 - - - +
1083C GLU* 3.7 24.5 + - - +
1085C MET 4.8 1.0 + - - -
1087C TYR* 3.0 59.3 - - - +
1091C GLY 4.4 7.3 + - - -
1093C PRO* 4.5 9.7 - - - +
1215C GLY* 4.5 5.5 + - - -
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 2.9 21.6 + - - +
42A ALA 3.1 8.9 + - - +
44A ARG* 1.3 79.9 - - - +
46A ILE* 1.3 66.8 + - + +
48A LEU* 3.3 2.3 + - - +
49A SER* 2.9 27.9 + - - +
34B GLY* 3.0 32.1 + - - +
35B PHE* 5.5 1.6 - - + -
37B HIS* 3.4 10.7 + - - +
38B THR* 3.2 37.7 - - + +
1083C GLU* 3.4 36.1 - - + +
1084C ASP* 4.5 7.7 + - - -
1215C GLY 3.0 20.2 + - - -
1216C ARG* 2.4 38.2 + - - +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.0 19.2 + - + +
43A LEU* 4.0 3.4 - - + +
45A ARG* 1.3 75.8 - - + +
47A LEU* 1.3 65.2 + - - +
49A SER* 3.4 3.4 - - - -
50A SER* 2.9 43.7 + - - +
51A MET* 3.9 3.7 + - - +
220A ALA* 3.9 35.7 - - + +
223A ILE* 4.0 17.0 - - + -
224A LEU* 5.2 15.0 - - + -
35B PHE* 3.5 33.2 - - + -
38B THR* 4.6 14.8 - - + +
39B LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 2.9 39.9 + - + +
44A ARG* 3.5 7.0 - - - +
46A ILE* 1.3 77.0 - - - +
48A LEU* 1.3 64.3 + - - +
51A MET* 2.9 41.9 + - + +
180A VAL* 3.1 16.7 - - + +
183A ILE* 4.0 34.8 - - + -
203A ILE* 4.9 8.5 - - + -
205A MET* 5.7 2.2 - - + -
216A ALA* 4.2 28.7 - - + +
217A ILE* 4.8 11.4 - - + +
220A ALA* 4.6 7.2 - - + -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.0 63.9 + - + +
45A ARG 4.0 1.8 - - - +
47A LEU* 1.3 77.6 - - - +
49A SER* 1.3 62.2 + - - +
178A SER* 4.3 13.5 + - - -
180A VAL* 4.0 10.9 - - + +
181A GLU 4.3 20.4 - - - +
182A ARG* 4.9 2.7 - - - -
183A ILE* 4.2 19.5 - - + +
821C ARG* 5.2 1.6 - - - +
1082C ILE* 4.1 32.7 - - + +
1083C GLU* 4.1 18.2 - - + +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 2.9 18.9 + - - -
46A ILE* 3.0 9.7 + - - -
48A LEU* 1.3 80.1 - - - +
50A SER* 1.3 75.0 + - - +
51A MET 3.7 0.8 + - - -
151A GLY* 4.3 17.2 + - - -
178A SER* 6.1 0.9 - - - -
33B ARG 5.2 5.4 - - - -
35B PHE* 4.0 13.6 - - - -
1083C GLU* 3.2 25.1 - - - -
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Residues in contact with SER 50 (chain A).
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* 2.9 33.8 + - - +
49A SER* 1.3 81.9 + - - +
51A MET* 1.3 66.3 + - - +
52A PRO* 3.2 9.4 - - - +
150A ARG* 4.2 19.0 - - - +
151A GLY 5.5 0.7 - - - -
223A ILE* 4.0 5.6 - - - +
6B THR 5.8 0.7 + - - -
8B PHE* 3.6 34.2 - - - -
32B GLU* 6.5 0.2 - - - -
35B PHE* 4.3 5.6 - - - -
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Residues in contact with MET 51 (chain A).
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* 4.5 4.3 - - - +
47A LEU* 2.9 47.0 + - + +
48A LEU 5.2 0.2 + - - -
49A SER 3.7 1.4 - - - -
50A SER* 1.3 76.8 - - - +
52A PRO* 1.3 75.9 - - + +
53A GLY 3.4 0.7 + - - -
150A ARG* 4.8 1.0 - - - -
151A GLY 5.0 0.3 + - - -
177A TYR 3.8 9.2 - - - +
178A SER* 4.3 2.0 + - - +
179A PRO* 3.4 26.2 - - + +
180A VAL* 4.3 8.3 - - + -
211A ILE* 4.8 9.2 - - + -
216A ALA* 3.3 50.3 - - + +
219A ARG* 4.0 19.3 - - + +
220A ALA* 4.5 7.9 - - - -
223A ILE* 5.3 1.1 - - - -
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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
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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