Contacts of the helix formed by residues 40 - 48 (chain A) in PDB entry 1EQB
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A THR* 1.3 80.5 + - - +
41A PRO* 1.3 74.4 - - - +
42A ARG* 3.3 12.6 + - - +
43A VAL* 3.0 18.8 + - - +
44A MET* 3.3 9.8 + - - +
232A ALA 4.5 1.0 + - - -
278A GLU* 2.9 38.9 + - - -
371A ARG* 3.7 8.2 - - - +
2B LEU* 4.1 11.2 - - - -
6B MET* 4.2 11.7 - - - -
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Residues in contact with PRO 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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40A SER* 1.3 87.6 - - - +
42A ARG* 1.3 56.2 + - - +
44A MET* 3.4 17.8 + - + +
45A GLN* 2.8 29.1 + - - +
416A TYR* 4.0 21.3 - - + -
2B LEU* 4.1 8.1 - - + -
3B LYS 3.4 21.5 - - - +
4B ARG* 4.1 14.8 - - - +
6B MET* 3.6 33.5 - - - +
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Residues in contact with ARG 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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40A SER* 3.0 7.6 - - - +
41A PRO* 1.3 78.6 - - - +
43A VAL* 1.3 60.7 + - - +
45A GLN* 3.5 2.0 + - - -
46A ALA* 3.3 18.0 + - - +
274A VAL* 3.9 16.9 - - + +
278A GLU* 2.7 37.5 + - - +
6B MET* 3.3 44.4 - - + +
7B ASN 2.9 33.1 + - - +
8B ILE* 3.4 22.5 - - + +
10B ASP* 4.7 4.0 + - - -
11B TYR* 3.0 52.5 - - - +
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Residues in contact with VAL 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 THR* 3.0 31.6 - - + +
40A SER* 3.0 14.1 + - - +
42A ARG* 1.3 74.1 - - - +
44A MET* 1.3 66.4 + - - +
46A ALA* 3.4 3.5 + - - +
47A GLN* 3.1 25.3 + - - +
232A ALA 5.0 0.2 - - - +
234A PRO* 3.5 37.0 - - + -
271A GLY* 3.9 4.7 - - - +
274A VAL* 3.7 21.8 - - + -
275A ALA* 3.8 22.4 - - + -
278A GLU* 4.4 2.5 - - - +
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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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39A THR* 3.9 13.0 - - + -
40A SER 3.3 5.6 + - - +
41A PRO* 3.4 32.5 - - + +
42A ARG 3.3 0.4 - - - -
43A VAL* 1.3 75.2 - - - +
45A GLN* 1.3 65.1 + - - +
47A GLN* 3.2 9.1 + - - +
48A GLY* 3.0 18.5 + - - -
416A TYR* 3.5 36.6 - - + +
4B ARG* 5.6 4.7 - - - +
48B GLY* 3.4 26.8 - - - +
49B SER 3.8 18.8 - - - +
50B GLN* 4.0 21.5 - - + -
52B THR* 4.2 10.3 - - + -
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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 PRO 2.8 15.8 + - - +
42A ARG 3.5 7.4 - - - +
43A VAL 3.3 0.2 - - - -
44A MET* 1.3 77.1 - - - +
46A ALA* 1.3 62.6 + - - +
48A GLY* 3.2 11.5 + - - -
49A SER* 3.5 10.2 + - - -
6B MET 4.0 3.8 - - - +
7B ASN* 3.3 30.9 - - - +
8B ILE* 3.5 21.5 + - + +
9B ALA* 4.6 1.0 - - - +
16B TRP* 3.5 32.9 - - + -
19B MET* 4.8 1.0 - - + +
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Residues in contact with ALA 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 ARG 3.3 10.0 + - - +
43A VAL 3.6 8.1 - - - +
45A GLN* 1.3 79.5 - - - +
47A GLN* 1.3 57.6 + - - +
49A SER* 2.7 31.5 + - - -
267A HIS* 3.7 6.9 - - - +
270A ALA* 3.9 12.1 - - + +
271A GLY* 3.5 31.2 - - - +
274A VAL* 4.9 1.1 - - + -
8B ILE* 3.8 8.4 - - + +
15B LEU* 5.5 0.4 - - + -
19B MET* 4.0 14.1 - - + -
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Residues in contact with GLN 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 VAL* 3.1 16.9 + - + +
44A MET* 3.2 8.1 + - - +
46A ALA* 1.3 79.7 - - + +
48A GLY* 1.3 57.8 + - - +
49A SER 3.3 1.3 + - - +
234A PRO* 3.1 30.2 - - + +
235A ARG 4.2 1.4 + - - +
267A HIS* 3.3 36.0 + - - +
268A VAL* 3.8 20.6 - - + +
271A GLY* 5.2 0.4 - - - -
47B GLN* 3.5 29.7 + - + +
52B THR* 3.4 28.6 + - - +
267B HIS* 3.4 28.9 + - + +
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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 MET 3.0 12.8 + - - -
45A GLN 3.7 7.0 - - - -
46A ALA 3.0 0.8 + - - -
47A GLN* 1.3 76.0 - - - +
49A SER* 1.3 63.2 + - - +
44B MET* 3.5 41.0 - - - +
48B GLY* 4.0 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