Contacts of the helix formed by residues 31 - 47 (chain A) in PDB entry 6I4X
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 MET 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 1.3 76.7 - - - +
32A GLN* 1.3 66.6 + - - +
33A ALA* 3.2 6.7 - - + +
34A ALA* 3.1 11.7 + - + +
35A ARG* 3.1 18.6 + - - -
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Residues in contact with GLN 32 (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 MET* 1.3 75.8 - - - +
33A ALA* 1.3 58.9 + - - +
35A ARG* 3.1 17.4 + - - +
36A LEU* 2.8 29.2 + - + +
99A TYR* 3.2 36.0 - - + +
101A ASP* 3.6 10.6 - - - +
102A GLY* 3.2 27.1 + - - +
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Residues in contact with ALA 33 (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 MET* 3.2 5.2 - - + +
32A GLN* 1.3 79.0 - - - +
34A ALA* 1.3 62.2 + - - +
36A LEU* 3.5 8.5 + - - +
37A ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 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 SER* 5.0 6.7 - - - -
31A MET* 3.1 18.3 + - + +
33A ALA* 1.3 75.8 - - - +
35A ARG* 1.3 66.2 + - - +
37A ALA* 3.2 7.4 + - - +
38A LYS* 3.1 23.8 + - - +
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Residues in contact with ARG 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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30A SER* 3.5 37.3 + - - -
31A MET 3.1 9.3 + - - +
32A GLN* 3.1 19.0 + - - +
34A ALA* 1.3 77.5 - - - +
36A LEU* 1.3 60.9 + - - +
38A LYS* 3.5 8.8 + - - +
39A ALA* 3.2 21.7 + - - +
99A TYR* 4.9 2.9 - - - +
101A ASP 4.2 4.6 + - - -
102A GLY* 3.2 25.0 + - - +
103A LYS* 4.6 5.1 - - - +
120A ASP* 2.8 55.5 + - + +
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Residues in contact with LEU 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 GLN* 2.8 15.9 + - + +
33A ALA* 3.8 7.9 - - - +
35A ARG* 1.3 70.8 - - - +
37A ALA* 1.3 65.4 + - - +
39A ALA* 3.3 3.3 + - - +
40A LEU* 3.0 41.5 + - + +
81A LEU* 4.4 18.2 - - + -
99A TYR* 3.4 38.1 + - + +
104A PHE* 3.5 32.5 - - + -
120A ASP 5.5 0.7 - - - -
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Residues in contact with ALA 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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33A ALA 3.1 17.6 + - - +
34A ALA* 3.2 8.3 + - - +
36A LEU* 1.3 77.5 - - - +
38A LYS* 1.3 63.5 + - - +
40A LEU* 3.2 11.8 + - - +
41A ARG* 3.1 23.0 + - - +
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Residues in contact with LYS 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 ALA 3.1 17.1 + - - +
35A ARG* 3.9 8.7 - - - +
37A ALA* 1.3 76.0 - - - +
39A ALA* 1.3 62.1 + - - +
40A LEU 3.5 0.3 + - - -
41A ARG* 3.5 7.2 + - + +
42A GLU* 3.2 38.9 + - + +
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Residues in contact with ALA 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 ARG 3.2 10.7 + - - +
36A LEU* 3.5 9.0 - - + +
37A ALA 3.2 0.4 - - - -
38A LYS* 1.3 79.5 - - - +
40A LEU* 1.3 61.0 + - - +
42A GLU* 3.7 14.2 + - - +
43A LEU* 3.4 17.3 + - - +
104A PHE* 4.0 17.9 - - + -
120A ASP 3.4 26.7 - - - +
121A SER* 4.0 8.7 - - - +
122A VAL* 4.3 10.6 - - + +
123A VAL* 4.8 0.7 - - - +
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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 LEU* 3.0 48.0 + - + +
37A ALA* 3.2 8.5 + - - +
39A ALA* 1.3 76.1 - - - +
41A ARG* 1.3 64.5 + - - +
43A LEU* 3.3 35.4 + - + +
44A GLY* 3.4 5.2 + - - -
81A LEU* 5.3 9.0 - - + -
82A LEU* 5.0 12.6 - - + -
104A PHE* 5.3 3.4 - - + -
122A VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 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 ALA 3.1 15.4 + - - +
38A LYS* 3.9 8.3 - - + +
39A ALA 3.4 0.4 - - - -
40A LEU* 1.3 74.6 - - - +
42A GLU* 1.3 66.0 + - + +
44A GLY* 3.2 11.3 + - - -
45A GLN* 3.4 14.5 + - - +
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Residues in contact with GLU 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 LYS* 3.2 36.5 + - + +
39A ALA* 4.0 6.7 - - - +
40A LEU 3.3 0.4 - - - -
41A ARG* 1.3 74.1 - - + +
43A LEU* 1.3 65.9 + - - +
45A GLN* 2.9 20.7 + - - +
46A THR* 3.3 14.4 + - - +
121A SER* 2.9 31.7 + - - -
123A VAL* 4.0 9.4 - - + +
193A GLU 4.5 14.4 - - - +
194A TYR* 4.0 6.1 - - + -
196A PHE* 3.7 22.4 - - + -
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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 ALA 3.4 11.2 + - - +
40A LEU* 3.3 24.0 + - + +
41A ARG 3.2 0.2 - - - -
42A GLU* 1.3 78.7 - - - +
44A GLY* 1.3 56.8 + - - +
46A THR* 2.7 29.0 + - + +
48A TRP* 5.1 1.8 - - + -
49A TYR* 3.5 31.5 - - + +
72A ILE* 3.6 37.9 - - + -
82A LEU* 3.8 35.9 - - + -
122A VAL* 4.2 11.9 - - + -
123A VAL* 3.9 12.0 - - + +
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Residues in contact with GLY 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 3.4 5.3 + - - -
41A ARG 3.2 8.8 + - - -
42A GLU 3.2 0.4 - - - -
43A LEU* 1.3 77.8 - - - +
45A GLN* 1.3 62.7 + - - +
46A THR 3.3 0.6 + - - -
47A GLY* 4.4 4.7 + - - -
49A TYR* 4.7 12.1 - - - -
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Residues in contact with GLN 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 ARG 3.4 10.7 + - - +
42A GLU* 2.9 14.1 + - - +
44A GLY* 1.3 78.1 + - - +
46A THR* 1.3 62.5 + - - +
47A GLY 3.6 0.2 - - - -
165A HIS* 3.3 24.4 + - - +
168A ARG* 3.1 25.2 + - - +
190A TYR* 4.7 4.2 + - - -
193A GLU* 5.6 5.2 - - + +
194A TYR* 4.0 16.8 - - + -
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Residues in contact with THR 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 GLU 3.3 16.8 - - - +
43A LEU* 2.7 20.4 + - + +
44A GLY 3.3 0.2 - - - -
45A GLN* 1.3 81.1 - - - +
47A GLY* 1.3 66.1 + - - +
48A TRP* 3.4 51.5 + - + -
49A TYR* 3.8 6.8 + - - +
123A VAL* 3.7 16.2 - - + -
157A TYR* 3.7 11.1 - - - -
161A PRO* 5.2 0.7 - - - +
165A HIS* 3.7 11.8 + - - -
169A LEU* 5.7 0.2 - - - +
194A TYR* 3.3 23.6 - - + +
198A VAL* 5.3 0.2 - - - +
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Residues in contact with GLY 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 4.5 0.2 + - - -
44A GLY 4.4 5.3 + - - -
45A GLN 3.6 1.6 - - - -
46A THR* 1.3 79.9 + - - +
48A TRP* 1.3 57.4 + - - +
49A TYR* 3.6 3.9 - - - +
157A TYR* 3.2 15.6 - - - -
158A THR* 2.9 34.6 + - - +
159A SER 4.5 2.9 + - - +
161A PRO* 5.6 4.9 - - - -
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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