Contacts of the helix formed by residues 33 - 48 (chain A) in PDB entry 6LGV
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 TYR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLY 3.5 25.4 - - - -
30A ILE* 2.7 23.5 + - + +
32A PRO* 1.3 86.2 - - + +
34A VAL* 1.3 65.2 + - - +
35A GLY 3.3 2.2 - - - -
36A PRO* 3.2 18.2 - - + +
37A LEU* 2.9 31.0 + - + +
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Residues in contact with VAL 34 (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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30A ILE 3.5 1.8 + - - +
31A GLY* 3.3 16.1 + - - +
33A TYR* 1.3 77.6 - - - +
35A GLY* 1.3 64.0 + - - +
37A LEU* 3.3 10.1 + - + +
38A LEU* 2.8 29.9 + - + +
200A ILE* 4.2 24.0 - - + -
203A ALA* 3.6 31.2 - - + -
204A VAL* 4.4 16.2 - - + -
261A GLY 4.7 1.1 - - - +
265A THR* 3.3 24.9 - - + +
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Residues in contact with GLY 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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32A PRO 4.6 1.8 + - - -
34A VAL* 1.3 77.0 - - - +
36A PRO* 1.3 63.7 - - - +
38A LEU* 2.9 14.4 + - - +
39A MET* 2.9 33.5 + - - +
163A ILE* 4.3 10.8 - - - +
265A THR* 4.8 12.4 + - - +
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Residues in contact with PRO 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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32A PRO 3.9 7.2 - - - +
33A TYR* 3.2 31.6 - - + +
35A GLY* 1.3 88.2 - - - +
37A LEU* 1.3 61.4 + - + +
39A MET* 3.1 20.6 + - + +
40A LEU* 2.9 22.9 + - - +
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Residues in contact with LEU 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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30A ILE* 4.2 14.6 - - + -
33A TYR* 2.9 27.5 + - + +
34A VAL* 3.5 5.4 - - - +
36A PRO* 1.3 76.6 - - + +
38A LEU* 1.3 61.8 + - - +
40A LEU* 3.1 11.2 + - + +
41A ILE* 3.0 23.6 + - - +
196A CYS* 4.1 28.9 - - + +
199A ALA* 3.6 29.6 - - + -
200A ILE* 3.7 28.0 - - + +
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Residues in contact with LEU 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 VAL* 2.8 23.1 + - + +
35A GLY* 3.4 7.2 - - - +
37A LEU* 1.3 72.7 - - - +
39A MET* 1.3 57.8 + - - +
41A ILE* 3.1 6.4 + - + +
42A MET* 2.8 38.3 + - + +
163A ILE* 3.8 19.3 - - + -
200A ILE* 3.6 21.3 - - + -
259A ASN* 4.0 11.4 - - - +
261A GLY* 3.6 26.2 - - - +
262A LEU* 3.7 9.9 - - + +
265A THR* 3.7 15.7 - - + +
401A CIT 3.7 30.7 - - + +
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Residues in contact with MET 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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35A GLY 2.9 18.3 + - - +
36A PRO* 3.1 24.0 + - - +
38A LEU* 1.3 75.1 - - - +
40A LEU* 1.3 57.2 + - - +
42A MET 3.2 0.5 + - - -
43A PHE* 2.8 28.1 + - - +
162A GLN* 3.7 33.9 - - + +
163A ILE* 3.6 30.5 + - + +
166A ILE* 5.6 4.3 - - + -
167A PRO* 3.4 19.9 - - + +
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Residues in contact with LEU 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 PRO 2.9 12.6 + - - +
37A LEU* 3.4 13.7 - - + +
38A LEU 3.1 0.4 - - - -
39A MET* 1.3 77.6 - - - +
41A ILE* 1.3 57.9 + - - +
43A PHE* 3.3 16.8 + - + +
44A ALA* 3.0 27.9 + - - +
192A MET* 6.4 2.5 - - + -
196A CYS* 3.6 25.4 - - - -
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Residues in contact with ILE 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 LEU 3.0 14.2 + - - +
38A LEU* 3.1 8.3 + - + +
40A LEU* 1.3 74.8 - - - +
42A MET* 1.3 58.5 + - - +
44A ALA* 3.3 7.7 + - - +
45A MET* 3.0 26.0 + - - +
106A THR* 3.4 10.5 - - - +
107A ALA* 4.7 10.8 - - + -
193A SER* 4.4 18.3 + - - +
196A CYS* 3.8 19.3 - - + -
197A ILE* 3.8 21.3 - - + -
200A ILE* 3.6 31.2 - - + -
401A CIT 3.3 29.4 - - + +
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Residues in contact with MET 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 LEU* 2.8 23.9 + - + +
39A MET 3.6 4.7 - - - +
41A ILE* 1.3 75.2 - - - +
43A PHE* 1.3 60.0 + - - +
45A MET* 3.2 10.8 + - + +
46A GLY 2.9 23.9 + - - -
106A THR* 3.6 39.0 - - + -
130A THR* 4.0 4.7 - - + +
163A ILE* 3.6 22.2 - - + +
164A VAL* 3.4 38.8 - - + +
167A PRO* 3.9 8.5 - - + -
168A ILE* 3.6 23.8 - - + +
259A ASN* 4.2 11.7 - - - +
401A CIT 4.5 2.5 - - - +
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Residues in contact with PHE 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 MET 2.8 20.4 + - - +
40A LEU* 3.6 19.1 - - + +
42A MET* 1.3 72.8 - - - +
44A ALA* 1.3 62.3 + - + +
46A GLY 3.1 0.9 + - - +
47A VAL* 2.8 54.1 + - + +
167A PRO* 3.6 27.7 - - + +
170A ALA* 3.9 14.4 - - + -
171A GLY* 3.5 23.1 - - - -
174A ILE* 4.4 15.3 - - + -
189A LEU* 6.2 3.4 - - + -
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Residues in contact with ALA 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 LEU 3.0 14.0 + - - +
41A ILE 3.5 8.5 - - - +
42A MET 3.3 0.2 - - - -
43A PHE* 1.3 80.7 - - + +
45A MET* 1.3 64.1 + - - +
47A VAL* 3.4 22.1 - - - +
48A THR* 3.4 13.2 + - - +
189A LEU* 4.1 22.5 - - + +
193A SER* 3.8 20.2 - - - +
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Residues in contact with MET 45 (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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41A ILE 3.0 14.6 + - - +
42A MET* 3.6 18.8 - - + +
43A PHE 3.2 0.2 - - - -
44A ALA* 1.3 77.2 - - - +
46A GLY* 1.3 63.8 + - - +
48A THR* 3.3 17.5 + - - +
49A LEU* 3.5 33.7 - - + +
106A THR* 3.6 47.8 - - + +
123A VAL 5.8 0.4 - - - +
126A SER* 4.5 11.9 - - - +
127A ALA* 4.7 9.6 - - - -
130A THR* 3.8 16.6 - - - +
168A ILE* 4.1 10.5 - - + -
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Residues in contact with GLY 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 MET 2.9 14.8 + - - -
43A PHE 3.7 1.6 - - - -
45A MET* 1.3 77.1 - - - +
47A VAL* 1.3 61.7 + - - +
49A LEU* 3.2 30.9 + - - +
168A ILE* 4.0 22.0 - - - -
171A GLY 3.8 8.3 - - - +
172A LEU* 3.7 11.4 - - - +
175A HIS* 4.9 0.2 - - - +
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Residues in contact with VAL 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 PHE* 2.8 44.2 + - + +
44A ALA* 3.4 15.9 - - - +
46A GLY* 1.3 72.9 - - - +
48A THR* 1.3 60.8 + - + +
49A LEU 3.5 0.2 - - - -
171A GLY* 3.4 23.2 - - - +
174A ILE* 4.0 4.9 - - + -
175A HIS* 2.8 27.9 + - - +
182A VAL* 3.3 32.0 - - + +
185A ILE* 5.6 2.5 - - + -
189A LEU* 3.7 23.8 - - + -
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Residues in contact with THR 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 ALA 3.4 14.6 + - - +
45A MET* 3.3 13.7 + - - +
46A GLY 3.2 0.4 - - - -
47A VAL* 1.3 79.6 - - + +
49A LEU* 1.3 66.1 + - - +
50A ARG* 3.5 11.6 + - - +
53A ASP* 4.2 2.4 - - - +
123A VAL* 6.0 3.3 - - - +
175A HIS* 4.2 1.6 - - - -
186A GLU* 3.7 31.1 - - + +
189A LEU* 3.4 26.5 - - + -
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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