Contacts of the helix formed by residues 30 - 48 (chain A) in PDB entry 1IN7
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 GLN 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.8 15.9 - - + -
29A GLY* 1.3 73.6 - - - +
31A GLU* 1.3 59.8 + - - +
32A ASN 3.3 2.5 - - - -
33A VAL* 3.2 28.2 + - + +
34A LYS* 2.9 27.0 + - + +
176A GLU 4.5 0.7 - - - +
177A LEU* 3.8 22.7 - - + +
178A ASP* 2.8 31.5 + - - +
179A PHE 4.6 2.4 + - - -
180A TYR* 3.3 45.3 - - + +
184A GLU* 4.1 7.3 + - - -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 3.2 16.2 + - - +
30A GLN* 1.3 77.3 - - - +
32A ASN* 1.3 65.5 + - - +
34A LYS* 2.9 32.8 + - - +
35A LYS* 3.0 47.9 + - - +
184A GLU* 5.0 6.7 + - - +
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Residues in contact with ASN 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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30A GLN 3.3 0.8 - - - -
31A GLU* 1.3 79.9 - - - +
33A VAL* 1.3 65.0 + - + +
35A LYS* 3.5 12.9 + - - +
36A LYS* 3.2 46.6 + - - +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN* 3.2 27.8 + - + +
32A ASN* 1.3 81.2 - - + +
34A LYS* 1.3 60.3 + - + +
36A LYS* 3.3 11.0 + - + +
37A LEU* 2.9 29.6 + - + +
67A LEU* 4.1 24.0 - - + -
175A LEU* 3.9 37.1 - - + +
176A GLU 3.7 25.4 - - - +
177A LEU* 4.6 4.3 - - + -
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Residues in contact with LYS 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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24A LEU* 3.9 38.5 + - + +
27A PHE* 3.0 41.2 + - + +
28A ILE* 4.5 0.8 - - - +
29A GLY 2.9 19.9 + - - +
30A GLN* 2.9 16.2 + - + +
31A GLU* 2.9 36.4 + - - +
33A VAL* 1.3 78.1 - - + +
35A LYS* 1.3 58.5 + - + +
37A LEU* 4.6 4.0 - - - +
38A SER* 2.8 34.8 + - - -
67A LEU* 5.4 0.4 - - + -
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Residues in contact with LYS 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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31A GLU* 3.0 39.3 + - - +
32A ASN* 3.8 13.2 + - - +
34A LYS* 1.3 75.5 - - + +
36A LYS* 1.3 64.6 + - + +
38A SER* 3.8 4.4 - - - -
39A LEU* 3.0 24.9 + - - +
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Residues in contact with LYS 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 ASN* 3.2 34.0 + - - +
33A VAL* 3.7 5.8 - - + +
35A LYS* 1.3 80.9 - - + +
37A LEU* 1.3 63.3 + - - +
39A LEU* 3.4 8.5 + - - +
40A ALA* 3.3 19.9 + - - +
173A ILE* 5.6 4.5 - - + +
174A ILE 5.3 5.6 + - - +
175A LEU* 4.0 23.1 - - + +
176A GLU 6.2 0.4 - - - +
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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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24A LEU* 4.4 11.4 - - + -
33A VAL* 2.9 18.8 + - + +
34A LYS* 4.1 2.9 - - - +
36A LYS* 1.3 76.4 - - - +
38A SER* 1.3 57.3 + - - +
40A ALA* 3.4 3.5 + - + -
41A LEU* 2.8 41.5 + - + +
51A LEU* 4.8 8.1 - - + -
54A VAL* 4.5 14.1 - - + -
67A LEU* 4.3 24.9 - - + +
70A ILE* 5.8 1.1 - - + -
71A ILE* 3.8 41.1 - - + +
173A ILE* 5.2 5.6 - - + -
175A LEU* 4.0 25.9 - - + +
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Residues in contact with SER 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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24A LEU* 3.9 18.7 - - - +
34A LYS 2.8 23.8 + - - -
35A LYS* 3.8 5.8 - - - -
37A LEU* 1.3 74.2 - - - +
39A LEU* 1.3 57.7 + - - +
41A LEU* 4.3 4.0 - - - -
42A GLU* 2.9 39.4 + - - +
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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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35A LYS 3.0 17.9 + - - +
36A LYS* 3.6 7.9 - - - +
37A LEU 3.3 0.2 - - - -
38A SER* 1.3 76.2 - - - +
40A ALA* 1.3 63.9 + - + +
42A GLU* 4.2 2.0 - - - +
43A ALA* 3.2 28.9 + - + +
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Residues in contact with ALA 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 LYS 3.3 9.7 + - - +
37A LEU* 4.0 5.6 - - + +
39A LEU* 1.3 78.8 - - + +
41A LEU* 1.3 61.5 + - - +
43A ALA* 3.8 5.2 - - - +
44A ALA* 3.0 24.3 + - - +
51A LEU* 3.4 16.0 - - + +
173A ILE* 3.5 32.3 - - + -
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Residues in contact with LEU 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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24A LEU* 4.7 15.0 - - + -
37A LEU* 2.8 33.7 + - + +
38A SER* 3.9 2.9 - - - +
40A ALA* 1.3 70.7 - - - +
42A GLU* 1.3 66.0 + - - +
44A ALA* 3.4 2.8 + - - +
45A LYS* 3.0 32.6 + - + +
51A LEU* 3.9 21.9 - - + +
70A ILE* 4.8 1.3 - - + +
71A ILE* 4.0 20.6 - - + +
74A GLU* 3.5 33.4 - - + -
75A LEU* 3.7 31.4 - - + -
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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 SER* 2.9 24.4 + - - +
39A LEU* 4.2 2.5 - - - +
41A LEU* 1.3 72.8 - - - +
43A ALA* 1.3 64.3 + - - +
45A LYS* 3.2 25.7 + - - +
46A MET* 2.9 51.6 + - - +
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Residues in contact with ALA 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* 3.2 22.3 + - + +
40A ALA* 3.8 6.3 - - - +
41A LEU 3.3 0.2 - - - -
42A GLU* 1.3 79.9 - - - +
44A ALA* 1.3 63.5 + - - +
46A MET* 3.3 9.2 + - - +
47A ARG* 3.0 38.1 + - - +
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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 ALA 3.0 18.4 + - - +
41A LEU 3.8 3.8 - - - +
43A ALA* 1.3 77.1 - - - +
45A LYS* 1.3 57.0 + - - +
47A ARG* 3.5 1.5 + - - +
48A GLY* 2.8 23.6 + - - -
49A GLU* 2.9 37.1 + - + +
50A VAL 4.7 0.9 - - - +
51A LEU* 4.1 24.9 - - + +
75A LEU* 4.6 4.9 - - + -
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Residues in contact with LYS 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 LEU* 3.0 30.9 + - + +
42A GLU* 3.4 24.6 + - - +
43A ALA 3.2 0.2 - - - -
44A ALA* 1.3 74.4 - - - +
46A MET* 1.3 67.0 + - + +
48A GLY* 3.0 14.5 + - - -
74A GLU* 2.8 53.3 + - - +
75A LEU* 4.1 15.9 - - + -
76A GLN* 5.1 10.6 - - - +
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Residues in contact with MET 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* 2.9 46.5 + - - +
43A ALA* 3.8 7.4 - - - +
45A LYS* 1.3 77.3 - - + +
47A ARG* 1.3 62.6 + - + +
48A GLY 3.7 0.2 + - - -
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Residues in contact with ARG 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 ALA* 3.0 27.2 + - - +
44A ALA* 4.2 1.3 - - - +
46A MET* 1.3 81.2 - - + +
48A GLY* 1.3 64.3 + - - +
49A GLU* 3.3 41.7 + - + +
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Residues in contact with GLY 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 2.8 7.9 + - - -
45A LYS* 3.0 12.4 + - - -
46A MET 3.3 0.4 + - - -
47A ARG* 1.3 79.2 - - - +
49A GLU* 1.3 60.4 + - - +
102A ARG* 5.8 1.7 + - - -
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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