Contacts of the helix formed by residues 26 - 37 (chain B) in PDB entry 2ERY
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 GLY 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GDP 3.0 30.7 + - - -
24B GLY 3.3 0.8 - - - -
25B VAL* 1.3 80.9 - - - +
27B LYS* 1.3 61.8 + - - +
28B SER 3.4 2.0 - - - -
30B LEU* 2.8 40.4 + - - +
92B VAL* 4.8 0.2 - - - -
127B ASN* 3.6 9.4 - - - -
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Residues in contact with LYS 27 (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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2B GDP 2.8 32.8 + - - +
19B VAL* 3.8 29.0 - - + +
20B VAL* 3.6 7.9 - - - +
21B GLY 3.1 30.5 + - - +
22B GLY 2.8 30.3 + - - -
23B GLY* 4.0 2.2 - - - -
25B VAL* 3.8 12.3 - - + +
26B GLY* 1.3 75.5 - - - +
28B SER* 1.3 61.9 + - - +
30B LEU* 3.8 3.8 - - - +
31B THR* 2.8 29.0 + - - -
68B ASP* 3.4 12.8 - - - +
69B THR* 3.2 26.7 - - - +
70B ALA* 4.8 4.5 - - - +
71B GLY 5.7 1.1 - - - +
92B VAL* 4.6 1.3 - - + -
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Residues in contact with SER 28 (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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2B GDP 3.1 10.8 + - - -
4B MG 2.1 31.1 - - - -
27B LYS* 1.3 79.8 - - - +
29B ALA* 1.3 58.7 + - - +
31B THR* 3.7 0.3 - - - -
32B ILE* 2.8 37.9 + - - +
40B VAL* 4.5 0.2 - - - -
43B TYR* 3.2 30.3 - - - -
68B ASP* 2.6 26.1 + - - -
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Residues in contact with ALA 29 (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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2B GDP 2.7 46.7 + - + +
26B GLY 4.0 0.7 - - - +
28B SER* 1.3 72.6 - - - +
30B LEU* 1.3 57.9 + - - +
32B ILE* 4.0 0.3 - - - +
33B GLN* 3.0 34.3 + - - +
38B TYR 4.7 0.5 - - - +
39B PHE* 3.9 13.0 - - + -
40B VAL* 3.9 19.2 - - + +
158B ALA* 3.6 12.6 - - + -
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Residues in contact with LEU 30 (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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19B VAL* 5.5 2.5 - - + -
26B GLY 2.8 27.6 + - - +
27B LYS 3.8 3.1 - - - +
29B ALA* 1.3 74.3 - - - +
31B THR* 1.3 55.9 + - - +
33B GLN* 3.4 2.0 + - - -
34B PHE* 2.9 29.9 + - - +
90B LEU* 5.7 4.3 - - + -
92B VAL* 3.9 35.2 - - + -
125B ILE* 4.3 10.5 - - + -
127B ASN* 3.5 30.5 - - + +
156B ALA* 4.2 10.5 - - + -
158B ALA* 3.9 16.6 - - + +
164B VAL* 3.6 23.4 - - + +
167B ALA* 6.4 1.8 - - + -
168B PHE* 4.5 11.7 - - + -
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Residues in contact with THR 31 (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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19B VAL* 3.7 19.2 - - - +
27B LYS 2.8 21.6 + - - -
28B SER* 3.7 3.4 - - - -
30B LEU* 1.3 75.2 - - - +
32B ILE* 1.3 59.0 + - - +
34B PHE* 3.1 7.1 + - + +
35B ILE* 2.9 32.0 + - + +
51B TYR* 3.4 38.4 - - + -
66B ILE* 3.9 19.1 - - + -
68B ASP* 3.8 14.3 - - + +
168B PHE* 4.4 5.4 - - + -
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Residues in contact with ILE 32 (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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28B SER* 2.8 25.7 + - - +
29B ALA 4.3 1.6 - - - +
31B THR* 1.3 69.7 - - - +
33B GLN* 1.3 60.6 + - - +
35B ILE* 4.9 2.7 - - - -
36B GLN* 2.7 37.2 + - - +
37B SER 3.3 3.6 + - - -
38B TYR* 3.4 43.3 - - + +
40B VAL* 3.7 27.8 - - + -
43B TYR* 3.8 33.2 - - + -
51B TYR* 3.9 22.4 - - + +
68B ASP* 5.7 0.4 - - - +
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Residues in contact with GLN 33 (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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29B ALA 3.0 20.5 + - - +
30B LEU* 3.7 4.3 - - - +
32B ILE* 1.3 76.3 - - - +
34B PHE* 1.3 62.0 + - - +
37B SER 3.0 27.5 + - - +
38B TYR* 3.4 19.5 + - - +
39B PHE* 3.8 17.5 - - - +
158B ALA* 2.9 30.7 + - - +
159B LYS 4.2 4.9 + - - -
161B ARG* 2.9 56.8 + - + +
164B VAL* 4.1 14.4 - - + -
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Residues in contact with PHE 34 (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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118A ASP* 3.5 18.8 - - - -
30B LEU 2.9 15.2 + - - +
31B THR* 3.1 8.3 + - - +
33B GLN* 1.3 79.7 - - - +
35B ILE* 1.3 80.5 + - + +
37B SER* 4.9 0.7 + - - -
53B LYS* 2.7 51.7 + - + -
55B CYS* 3.9 5.4 - - - -
64B LEU* 3.8 20.6 - - + -
66B ILE* 4.3 8.1 - - + -
161B ARG* 3.5 3.8 + - - +
164B VAL* 3.6 7.4 - - + +
165B ASP* 3.3 26.7 - - - -
168B PHE* 3.4 56.3 - + + -
169B HIS* 4.7 1.3 - + - -
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Residues in contact with ILE 35 (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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31B THR* 2.9 18.8 + - + +
32B ILE* 4.4 0.9 - - - +
34B PHE* 1.3 100.0 - - + +
36B GLN* 1.3 73.7 + - + +
37B SER* 5.2 1.2 + - - -
51B TYR* 3.6 38.6 - - + -
52B THR 3.8 19.3 - - - +
53B LYS* 3.7 28.9 - - + +
66B ILE* 4.5 6.3 - - + -
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Residues in contact with GLN 36 (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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32B ILE* 2.7 26.6 + - + +
35B ILE* 1.3 87.9 - - + +
37B SER* 1.3 69.9 + - - +
38B TYR* 3.0 38.1 + - + +
51B TYR* 4.0 24.3 - - + -
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Residues in contact with SER 37 (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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119A GLU* 3.8 19.1 + - - +
32B ILE 3.3 1.2 + - - -
33B GLN* 3.0 25.4 + - - -
34B PHE 4.9 1.0 + - - -
35B ILE 5.2 1.0 + - - -
36B GLN* 1.3 82.3 - - - +
38B TYR* 1.3 59.8 + - - +
53B LYS* 5.7 0.5 + - - -
161B ARG* 3.5 26.2 + - - -
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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