Contacts of the helix formed by residues 40 - 48 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.2 10.8 - - - -
6C MET* 4.1 11.4 - - - -
39D THR* 1.3 80.9 + - - +
41D PRO* 1.3 75.5 - - - +
42D ARG* 3.0 14.0 + - - +
43D VAL* 3.1 17.9 + - - +
44D MET* 3.3 10.2 + - - +
232D ALA 4.5 1.2 + - - -
278D GLU* 2.9 37.5 + - - -
371D ARG* 3.7 8.7 - - - +
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Residues in contact with PRO 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.1 12.8 - - + -
3C LYS 3.3 24.7 - - - +
4C ARG* 4.1 16.8 - - + +
6C MET* 3.8 24.2 - - + +
40D SER* 1.3 88.1 - - - +
42D ARG* 1.3 54.7 + - - +
43D VAL 3.3 0.2 - - - -
44D MET* 3.3 24.8 + - + +
45D GLN* 2.8 30.1 + - - +
416D TYR* 4.1 12.1 - - + -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 3.3 39.0 - - + +
7C ASN 3.1 31.4 + - - +
8C ILE* 3.6 15.8 - - + +
10C ASP* 4.8 3.6 + - - -
11C TYR* 3.0 59.5 - - - +
40D SER* 3.0 7.4 - - - +
41D PRO* 1.3 75.9 - - - +
43D VAL* 1.3 63.0 + - - +
45D GLN* 3.5 8.1 + - - +
46D ALA* 3.3 17.3 + - - +
274D VAL* 3.9 16.5 - - + +
278D GLU* 2.7 35.0 + - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D THR* 3.0 32.1 - - + +
40D SER* 3.1 12.4 + - - +
42D ARG* 1.3 74.2 - - - +
44D MET* 1.3 65.4 + - - +
46D ALA* 3.4 3.3 + - - +
47D GLN* 3.1 25.0 + - - +
232D ALA 5.0 0.4 - - - +
233D GLY* 4.7 0.2 - - - -
234D PRO* 3.5 37.2 - - + -
271D GLY* 4.0 5.4 - - - +
274D VAL* 3.8 21.8 - - + -
275D ALA* 3.9 21.8 - - + -
278D GLU* 4.3 3.1 - - - +
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Residues in contact with MET 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ARG* 5.4 4.3 - - - +
48C GLY* 3.4 28.5 - - - +
49C SER 3.8 25.4 - - - +
50C GLN* 4.1 17.0 - - + -
52C THR* 4.2 5.8 - - + -
53C ASN* 5.3 0.2 - - - -
39D THR* 3.9 13.2 - - + -
40D SER 3.7 5.6 - - - +
41D PRO* 3.3 33.4 + - + +
42D ARG 3.3 0.4 - - - -
43D VAL* 1.3 75.6 - - - +
45D GLN* 1.3 65.6 + - - +
47D GLN* 3.2 9.8 + - - +
48D GLY* 3.0 18.5 + - - -
416D TYR* 3.7 33.9 - - + +
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET 4.0 4.5 - - - +
7C ASN* 3.2 31.8 - - - +
8C ILE* 3.7 20.6 - - + +
9C ALA* 4.7 0.8 - - - +
16C TRP* 3.3 34.5 - - + -
19C MET* 4.8 1.4 - - + +
41D PRO 2.8 16.2 + - - +
42D ARG 3.5 7.2 - - - +
44D MET* 1.3 76.5 - - - +
46D ALA* 1.3 62.4 + - - +
48D GLY* 3.2 11.2 + - - -
49D SER* 3.5 10.2 + - - -
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.0 10.5 - - + +
19C MET* 4.0 11.4 - - + -
42D ARG 3.3 9.6 + - - +
43D VAL 3.5 8.3 - - - +
44D MET 3.2 0.4 - - - -
45D GLN* 1.3 79.1 - - - +
47D GLN* 1.3 58.2 + - - +
49D SER* 2.8 31.7 + - - -
267D HIS* 3.7 7.4 - - - +
270D ALA* 4.0 10.9 - - + +
271D GLY* 3.5 30.5 - - - +
274D VAL* 4.9 0.4 - - + -
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLN* 3.5 29.8 + - + +
49C SER 5.3 0.2 + - - -
52C THR* 3.4 29.0 + - - +
267C HIS* 3.4 27.6 + - + +
43D VAL* 3.1 18.4 + - - +
44D MET* 3.2 7.9 + - - +
46D ALA* 1.3 79.4 - - + +
48D GLY* 1.3 57.1 + - - +
49D SER 3.3 1.7 + - - +
234D PRO* 3.2 29.6 - - + +
235D ARG 4.2 1.7 + - - +
267D HIS* 3.2 35.5 + - - +
268D VAL* 3.9 19.7 - - + +
271D GLY* 5.2 0.7 - - - -
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Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C MET* 3.4 41.2 - - - +
48C GLY* 4.1 5.2 - - - -
44D MET 3.0 12.5 + - - -
45D GLN* 3.2 7.6 + - - -
46D ALA 3.0 1.4 - - - -
47D GLN* 1.3 77.1 - - - +
49D SER* 1.3 62.6 + - - +
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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