Contacts of the helix formed by residues 31 - 45 (chain A) in PDB entry 2E2C
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 VAL 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.2 5.0 + - - +
30A SER* 1.3 73.3 + - - +
32A SER* 1.3 56.7 + - - +
34A ARG* 3.2 5.7 + - - +
35A LEU* 2.9 39.0 + - + +
60A PHE* 3.3 35.7 - - + -
85A PHE* 5.2 0.4 - - + -
86A PRO 4.4 0.7 - - - +
87A SER* 3.9 20.9 - - - +
89A TYR* 3.7 41.7 - - + +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.3 8.8 + - - -
31A VAL* 1.3 77.4 - - - +
33A LYS* 1.3 59.7 + - - +
35A LEU* 4.4 2.0 - - - -
36A GLN* 2.8 32.7 + - - +
59A LEU* 3.5 22.7 - - - +
60A PHE* 3.7 19.5 - - - -
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Residues in contact with LYS 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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28A ARG* 3.6 35.1 + - + +
29A HIS* 4.4 16.6 - - - +
30A SER* 3.0 20.5 + - - +
32A SER* 1.3 77.1 - - - +
34A ARG* 1.3 72.1 + - - +
36A GLN* 3.3 9.1 + - - +
37A GLN* 3.2 22.3 + - + +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 5.3 4.6 + - - -
29A HIS* 3.8 29.2 + - + +
30A SER 3.0 11.2 + - - +
31A VAL* 3.6 9.0 - - - +
33A LYS* 1.3 86.3 - - - +
35A LEU* 1.3 62.9 + - - +
37A GLN* 3.3 24.4 + - - +
38A GLU* 3.0 46.0 + - - +
89A TYR* 4.3 7.9 - - + -
90A PRO* 4.2 26.8 - - + +
91A TYR* 4.7 7.7 + - - -
124A ALA 5.6 1.8 + - - -
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Residues in contact with LEU 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 VAL* 2.9 37.5 + - + +
32A SER 3.8 4.7 - - - +
34A ARG* 1.3 77.6 - - - +
36A GLN* 1.3 56.8 + - - +
38A GLU* 3.4 4.3 + - - +
39A LEU* 2.9 30.4 + - - +
59A LEU* 3.3 44.2 - - + +
60A PHE* 4.3 12.6 - - + -
62A TRP* 3.6 16.7 - - + -
85A PHE* 3.6 36.6 - - + -
89A TYR* 3.7 17.5 - - + -
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Residues in contact with GLN 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 SER* 2.8 25.7 + - - +
33A LYS* 3.5 9.4 - - - +
34A ARG 3.3 0.2 - - - -
35A LEU* 1.3 76.4 - - - +
37A GLN* 1.3 56.5 + - - +
39A LEU* 3.2 18.4 + - - +
40A ARG* 3.0 46.0 + - - +
59A LEU* 3.8 19.2 - - - +
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Residues in contact with GLN 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 LYS 3.2 10.2 + - - +
34A ARG* 3.7 30.7 + - - +
36A GLN* 1.3 79.2 - - - +
38A GLU* 1.3 58.9 + - + +
40A ARG* 3.4 31.1 + - - +
41A THR* 3.0 44.6 + - + +
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Residues in contact with GLU 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 ARG* 3.0 34.1 + - - +
35A LEU* 3.7 6.2 - - - +
37A GLN* 1.3 75.0 - - + +
39A LEU* 1.3 60.4 + - - +
40A ARG 3.2 0.4 - - - -
41A THR* 2.9 19.0 + - - -
42A LEU* 3.0 19.8 + - - +
62A TRP* 4.3 8.0 - - + -
89A TYR* 2.8 42.9 + - - -
90A PRO* 4.7 1.9 - - - +
124A ALA 5.7 0.2 - - - +
126A TYR 4.0 4.0 - - - +
127A ASP* 3.6 24.4 - - + +
128A VAL* 2.9 26.9 + - + +
129A ARG* 5.8 0.9 + - - +
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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
----------------------------------------------------------
35A LEU 2.9 17.3 + - - +
36A GLN* 3.2 20.6 + - - +
38A GLU* 1.3 77.4 - - - +
40A ARG* 1.3 61.1 + - + +
42A LEU* 4.0 4.4 - - + +
43A LEU* 3.3 26.2 + - + +
52A ALA 3.5 24.9 - - - +
53A PHE* 4.2 10.3 - - + -
54A PRO* 3.6 35.2 - - + -
59A LEU* 4.7 4.3 - - + -
62A TRP* 3.8 22.4 - - + -
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Residues in contact with ARG 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 GLN* 3.0 38.2 + - + +
37A GLN* 3.6 32.9 - - - +
38A GLU 3.2 0.2 - - - -
39A LEU* 1.3 74.9 - - + +
41A THR* 1.3 57.7 + - + +
42A LEU 3.1 1.3 + - - -
43A LEU* 3.2 4.8 + - - +
44A MET* 2.8 46.2 + - + +
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Residues in contact with THR 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 GLN* 3.0 25.8 + - + +
38A GLU* 2.9 19.6 + - - +
40A ARG* 1.3 77.3 - - + +
42A LEU* 1.3 53.8 + - - +
44A MET* 4.1 4.8 - - - +
45A SER* 2.6 40.0 + - - -
127A ASP* 4.5 13.1 + - - -
129A ARG* 5.2 4.9 - - - +
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Residues in contact with LEU 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 GLU 3.0 18.6 + - - +
39A LEU* 4.0 4.7 - - + +
40A ARG 3.1 0.4 - - - -
41A THR* 1.3 76.3 + - - +
43A LEU* 1.3 65.0 + - - +
45A SER* 3.3 13.9 + - - -
46A GLY* 3.5 9.4 + - - -
47A ASP* 4.5 6.7 + - + +
50A ILE* 4.4 20.0 - - + +
51A THR* 6.1 0.7 - - - -
52A ALA* 3.4 42.4 - - + +
62A TRP* 4.2 16.4 - - + -
128A VAL* 4.3 9.2 - - + -
129A ARG* 3.9 35.4 - - + +
132A LEU* 4.4 1.8 - - + -
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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* 3.3 17.1 + - + +
40A ARG* 3.2 5.3 + - - +
42A LEU* 1.3 81.2 - - - +
44A MET* 1.3 68.9 + - + +
45A SER 3.7 0.2 + - - -
46A GLY* 3.8 9.2 + - - -
52A ALA 6.1 0.2 - - - +
53A PHE* 3.9 36.8 - - + -
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Residues in contact with MET 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 ARG* 2.8 32.9 + - + +
41A THR* 4.1 5.4 - - - +
43A LEU* 1.3 83.0 - - + +
45A SER* 1.3 64.8 + - - +
46A GLY* 4.3 0.9 - - - -
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.6 24.6 + - - -
42A LEU 3.3 5.6 + - - -
44A MET* 1.3 78.9 - - - +
46A GLY* 1.3 64.8 + - - +
47A ASP* 3.6 6.4 - - - +
129A ARG* 3.6 36.0 + - - -
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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