Contacts of the helix formed by residues 16 - 26 (chain B) in PDB entry 2Q4E
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 ASP 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP 5.0 1.4 - - - +
287A LEU* 5.4 0.7 - - - +
288A VAL* 5.9 2.4 - - - +
14B CYS 4.0 0.8 + - - -
15B ALA* 1.3 74.1 - - - +
17B ILE* 1.3 61.6 + - - +
18B ALA 3.0 1.3 + - - -
19B ARG* 2.7 63.6 + - - +
20B LYS 4.4 0.7 + - - -
47B PHE* 5.4 1.3 - - - -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 6.0 5.6 - - + -
15B ALA* 4.1 7.4 - - + -
16B ASP* 1.3 77.4 + - - +
18B ALA* 1.3 64.1 + - - +
19B ARG 3.2 0.8 + - - -
20B LYS* 3.5 26.9 + - + +
21B VAL* 3.4 17.8 + - + +
76B TYR* 3.6 19.1 - - - +
78B PRO* 3.7 18.6 - - + +
101B GLU* 4.0 13.5 - - + +
130B MSE 4.5 13.0 - - + -
174B ARG* 6.0 6.3 - - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.1 23.3 - - + -
15B ALA 2.9 25.2 + - - +
17B ILE* 1.3 80.3 - - - +
19B ARG* 1.3 54.6 + - - +
20B LYS 3.4 0.2 - - - -
21B VAL* 3.8 1.0 - - - +
22B SER* 2.6 39.5 + - - +
47B PHE* 3.7 15.0 - - + -
76B TYR* 3.8 16.7 - - + -
78B PRO* 4.3 3.1 - - + -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP* 3.0 51.3 + - - -
287A LEU* 3.7 30.3 - - + +
16B ASP* 2.7 43.8 + - - +
17B ILE 3.2 0.8 - - - -
18B ALA* 1.3 77.6 - - - +
20B LYS* 1.3 61.5 + - - +
22B SER* 3.3 19.0 + - - -
23B ARG* 3.4 7.4 + - - +
47B PHE* 4.1 11.9 - - + -
51B ASN* 3.1 37.6 - - - +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU* 3.6 41.4 - - + +
288A VAL* 3.2 24.4 + - + +
289A THR* 4.6 6.0 - - - +
16B ASP 4.4 0.8 + - - +
17B ILE* 3.5 21.3 + - + +
18B ALA 3.4 0.2 - - - -
19B ARG* 1.3 78.2 - - - +
21B VAL* 1.3 64.3 + - - +
23B ARG* 3.1 16.9 + - - +
24B ALA* 3.3 9.7 + - - +
130B MSE 3.5 32.2 - - + +
267B ILE* 3.8 18.4 - - - +
306B GLN* 5.3 1.8 - - - +
307B GLU* 3.1 37.9 + - + +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.4 9.9 + - + +
18B ALA 4.1 0.2 - - - +
19B ARG 3.4 0.4 - - - -
20B LYS* 1.3 74.7 - - - +
22B SER* 1.3 59.7 + - - +
24B ALA* 3.1 7.6 + - + +
25B ILE* 2.8 32.0 + - + +
76B TYR* 3.2 62.4 - - + +
99B LEU* 4.9 2.2 - - + -
101B GLU* 4.5 1.1 - - - +
130B MSE 4.4 22.2 - - + -
307B GLU* 5.4 2.5 - - + -
310B MSE 5.1 6.1 - - + -
311B VAL* 4.2 20.2 - - + -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.9 3.6 - - - +
18B ALA* 2.6 25.9 + - - +
19B ARG* 3.4 9.3 - - - -
20B LYS 3.1 0.2 - - - -
21B VAL* 1.3 77.9 - - - +
23B ARG* 1.3 60.2 + - - +
25B ILE* 3.2 19.6 + - - +
26B HIS* 3.4 10.4 + - - +
33B ILE* 3.9 11.9 - - - +
47B PHE* 4.7 1.0 - - - -
51B ASN* 5.6 3.8 - - - -
53B TYR* 2.7 40.9 + - - -
76B TYR* 5.8 0.2 - - - -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU* 5.1 14.2 - - + +
289A THR* 3.3 15.5 + - - +
19B ARG 3.4 7.3 + - - +
20B LYS* 3.1 12.2 + - - +
22B SER* 1.3 76.0 - - - +
24B ALA* 1.3 63.9 + - - +
26B HIS* 3.7 1.5 + - - +
27B LEU* 3.0 55.7 + - + +
271B GLU* 2.7 42.7 + - - -
305B PRO* 3.9 8.9 - - - +
307B GLU* 3.4 20.4 + - - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 3.3 2.0 + - - +
21B VAL* 3.1 13.4 + - - +
23B ARG* 1.3 77.0 - - - +
25B ILE* 1.3 67.5 + - - +
27B LEU* 3.4 9.1 + - - -
28B ALA 3.6 3.6 + - - -
307B GLU* 3.4 39.5 - - + +
308B ALA* 3.5 23.7 - - - +
311B VAL* 3.0 21.7 - - + +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.1 34.1 - - + -
11B VAL* 4.6 16.6 - - + -
21B VAL* 2.8 28.8 + - + +
22B SER* 3.2 15.9 + - - +
24B ALA* 1.3 77.0 - - - +
26B HIS* 1.3 58.7 + - - +
28B ALA* 3.2 12.6 - - - +
31B ALA* 3.1 19.2 - - - +
32B THR* 3.5 36.6 - - - +
33B ILE* 3.8 12.3 - - + -
76B TYR* 4.8 4.0 - - + -
99B LEU* 6.2 0.7 - - + -
311B VAL* 4.1 19.2 - - + +
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 3.4 9.4 + - - +
23B ARG 3.7 1.9 + - - +
24B ALA 3.4 0.2 - - - -
25B ILE* 1.3 78.4 - - + +
27B LEU* 1.3 59.1 + - - +
28B ALA* 2.7 10.6 + - + +
29B PRO* 5.1 8.9 - - + +
31B ALA 3.8 8.8 + - - -
32B THR* 2.9 37.7 + - - -
33B ILE* 4.4 8.3 - - + -
54B PRO* 6.3 2.0 - - + -
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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