Contacts of the strand formed by residues 17 - 30 (chain B) in PDB entry 1EQR
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 GLN 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B THR* 4.3 4.9 - - - +
15B GLY 3.7 3.6 + - - +
16B GLN* 1.3 79.0 + - - +
18B VAL* 1.3 69.5 + - - +
72B THR* 4.0 10.6 + - - +
73B GLY 3.3 16.4 - - - +
74B THR* 3.9 16.0 + - + +
97B SER* 3.7 20.4 + - - -
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Residues in contact with VAL 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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3B THR* 3.6 16.6 - - + -
4B GLU* 4.4 9.2 - - + +
9B LEU* 4.6 10.5 - - + -
16B GLN* 3.9 17.5 - - + +
17B GLN* 1.3 82.0 - - - +
19B THR* 1.3 62.7 + - - +
20B LEU* 3.8 31.9 - - + -
71B VAL 5.6 0.2 - - - +
72B THR* 3.0 8.7 + - - -
73B GLY 2.6 42.2 + - - +
75B VAL* 4.1 13.2 - - + -
94B VAL* 4.4 17.9 - - + -
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.2 24.2 - - - +
2B ARG* 3.3 3.1 - - - -
3B THR* 2.6 44.1 + - - +
4B GLU 3.5 6.1 + - - +
18B VAL* 1.3 72.7 - - - +
20B LEU* 1.3 63.8 + - - +
70B GLN* 3.8 29.4 - - + +
71B VAL 3.6 5.4 - - - +
72B THR* 3.4 18.5 + - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 3.2 35.9 - - + +
6B CYS* 3.9 29.8 - - - +
9B LEU* 4.1 14.1 - - + -
18B VAL* 3.8 26.5 - - + -
19B THR* 1.3 78.3 - - - +
21B CYS* 1.3 63.0 + - - +
38B MET* 3.1 23.6 - - + +
40B ASP* 5.6 0.2 - - - +
45B VAL* 4.0 15.0 - - + -
47B VAL* 5.9 0.9 - - + -
70B GLN* 3.3 4.0 - - - +
71B VAL* 2.8 39.8 + - + +
94B VAL* 4.5 12.3 - - + -
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Residues in contact with CYS 21 (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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238A PHE* 3.7 29.6 - - + -
1B MET 3.8 7.6 - - - -
2B ARG* 3.0 62.2 + - - +
4B GLU 5.0 0.2 + - - -
6B CYS* 4.7 0.3 - - - -
20B LEU* 1.3 77.1 - - - +
22B GLY* 1.3 58.2 + - - +
38B MET* 3.8 2.0 - - - -
40B ASP* 3.6 13.7 + - - +
69B ILE 3.7 4.5 - - - +
70B GLN* 3.3 30.3 - - - -
102B ILE* 5.1 0.4 - - - -
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.1 3.0 - - - -
21B CYS* 1.3 76.3 - - - +
23B TRP* 1.3 76.5 + - - -
38B MET* 3.5 11.4 - - - +
39B ARG 3.2 13.2 - - - -
40B ASP* 4.2 0.2 - - - -
68B CYS* 3.5 7.1 - - - -
69B ILE* 2.9 32.7 + - - +
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Residues in contact with TRP 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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202A MET 4.1 9.4 - - - -
203A MET 5.0 2.7 + - - -
205A GLY* 4.1 33.2 - - - -
206A PHE 5.2 1.1 - - - -
207A ASP* 5.8 1.8 - - + -
237A SER* 5.5 1.1 - - - -
238A PHE* 3.8 22.0 - + - -
524A GLY 3.0 20.8 + - - -
526A PRO* 3.8 28.5 - - + +
2B ARG* 5.3 0.9 - - - -
22B GLY* 1.3 84.2 - - - -
24B VAL* 1.3 63.6 + - - +
38B MET* 3.4 8.5 - - - +
39B ARG* 2.6 78.9 + - - +
40B ASP* 4.3 10.5 - - + -
66B GLU* 3.7 31.9 - - - +
67B PHE 3.1 8.7 - - - -
68B CYS* 3.7 7.9 - - + +
69B ILE* 5.1 0.7 - - - -
130B ARG* 4.0 11.8 - - - +
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Residues in contact with VAL 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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23B TRP* 1.3 74.1 - - - +
25B ASN* 1.3 60.7 + - - +
26B ARG 3.6 11.7 - - - +
27B ARG* 4.4 2.2 - - + -
36B ILE* 3.3 46.9 - - + -
37B ASP 4.0 2.0 - - - -
63B LEU* 4.2 5.8 - - + -
64B ARG 3.1 31.9 - - - +
65B ASN* 3.8 2.1 - - - +
66B GLU* 2.9 29.9 + - - +
67B PHE* 3.0 23.3 + - + +
69B ILE* 4.2 14.8 - - + -
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Residues in contact with ASN 25 (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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23B TRP 3.4 1.0 + - - -
24B VAL* 1.3 74.2 - - - +
26B ARG* 1.3 63.0 + - - +
37B ASP* 2.7 28.5 + - + +
39B ARG* 2.9 34.1 + - + +
44B ILE* 3.2 32.2 - - + +
65B ASN* 3.4 14.2 + - - +
66B GLU* 4.4 3.5 - - - +
132B PRO* 4.7 6.9 - - - +
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Residues in contact with ARG 26 (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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24B VAL* 3.6 4.0 - - - +
25B ASN* 1.3 82.4 - - - +
27B ARG* 1.3 63.4 + - - +
28B ARG* 2.7 62.4 - - - +
35B PHE* 5.7 5.5 + - - +
36B ILE* 3.2 9.5 - - - +
37B ASP* 3.0 60.7 + - + +
46B GLN* 5.4 5.3 + - - -
65B ASN* 3.5 8.5 - - - +
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Residues in contact with ARG 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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24B VAL* 4.4 4.5 - - + -
26B ARG* 1.3 75.4 - - - +
28B ARG* 1.3 83.9 + - - +
29B ASP* 2.6 38.1 + - - -
34B ILE* 3.4 13.9 - - + +
35B PHE 3.4 5.2 - - - +
36B ILE* 3.1 27.8 - - + -
60B ALA 3.4 12.3 + - - -
61B SER* 3.1 34.1 + - - +
63B LEU* 3.3 23.8 + - - +
64B ARG* 5.4 2.2 - - - -
65B ASN* 4.1 5.7 - - - +
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Residues in contact with ARG 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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26B ARG* 2.7 75.9 - - - +
27B ARG* 1.3 85.7 + - - +
29B ASP* 1.3 66.9 + - - +
35B PHE* 2.7 54.9 + - + +
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Residues in contact with ASP 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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27B ARG* 2.6 40.9 + - - -
28B ARG* 1.3 84.7 - - - +
30B LEU* 1.3 60.4 + - - +
31B GLY 3.7 17.4 + - - +
32B SER* 5.0 1.0 - - - +
33B LEU 3.3 2.9 - - - +
34B ILE* 3.6 20.9 - - - +
35B PHE* 5.3 1.1 - - - -
61B SER* 6.0 0.3 - - - -
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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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29B ASP* 1.3 72.7 - - - +
31B GLY* 1.3 61.8 + - - +
32B SER 3.0 0.9 + - - -
33B LEU* 2.8 53.8 + - + +
35B PHE* 4.3 23.5 - - + -
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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