Contacts of the strand formed by residues 37 - 48 (chain A) in PDB entry 5E67
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 TRP 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.7 30.3 - - + -
28A ARG 3.3 7.4 - - - -
29A LYS* 3.5 47.3 - - + +
30A ASN 3.8 1.0 + - - +
33A TYR* 3.5 16.8 - - - +
35A THR* 3.1 28.6 + - - -
36A GLY* 1.3 87.2 + - - +
38A LEU* 1.3 59.9 - - - +
39A VAL* 4.2 4.5 + - - +
122A HIS 5.2 2.3 - - - +
123A LEU* 5.9 2.1 - - - +
128A LEU* 3.7 25.6 - - + -
145A GLU* 3.9 23.3 - - + -
146A LEU* 3.6 19.7 - - + -
149A ALA* 3.6 32.3 - - + -
150A PHE* 3.8 11.4 - + - -
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Residues in contact with LEU 38 (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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26A ARG 3.6 1.4 - - - +
27A VAL* 3.3 2.9 - - - -
28A ARG* 2.6 66.3 + - + +
30A ASN* 4.8 7.4 - - + +
33A TYR* 3.5 50.4 - - + +
37A TRP* 1.3 72.4 - - - +
39A VAL* 1.3 78.0 + - - +
40A VAL* 3.8 15.4 + - + -
122A HIS* 6.3 0.4 - - + -
21B A 5.7 1.1 - - - +
4C A 4.7 6.7 - - + +
5C T 3.9 30.3 - - + +
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Residues in contact with VAL 39 (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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25A VAL* 4.7 2.5 - - + -
26A ARG 3.3 6.3 - - - +
27A VAL* 4.4 8.1 - - + -
37A TRP 4.2 3.6 + - - +
38A LEU* 1.3 83.3 - - - +
40A VAL* 1.3 66.7 + - - +
113A VAL* 4.5 4.0 - - + -
117A MET* 3.5 38.5 - - + +
122A HIS* 4.1 29.5 - - + +
128A LEU* 3.7 29.4 - - + -
131A ILE* 3.9 24.9 - - + -
4C A 5.6 0.2 + - - -
5C T 5.5 0.2 - - - +
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Residues in contact with VAL 40 (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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24A MET 4.1 0.2 - - - +
25A VAL* 3.4 4.9 - - - +
26A ARG* 2.8 45.7 + - + +
28A ARG* 4.8 10.3 - - - +
38A LEU* 3.8 15.3 - - + -
39A VAL* 1.3 81.0 - - - +
41A ALA* 1.3 64.9 + - - +
42A ILE* 3.8 26.0 - - + -
81A GLU* 4.5 17.5 - - + +
117A MET* 4.4 4.3 - - - -
5C T 3.8 29.2 - - + -
6C C 6.0 2.7 - - - +
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Residues in contact with ALA 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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24A MET 3.4 6.1 - - - +
25A VAL* 4.8 6.5 - - + -
40A VAL* 1.3 73.2 - - - +
42A ILE* 1.3 67.5 + - - +
81A GLU* 3.5 14.6 + - - +
83A SER* 5.1 1.6 + - - +
86A LEU* 3.2 16.2 - - + +
110A PHE* 3.8 20.2 - - + -
113A VAL* 5.0 2.0 - - + -
114A LEU* 3.9 27.8 - - + -
117A MET* 4.3 13.8 - - - +
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Residues in contact with ILE 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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22A SER 3.6 2.3 - - - +
24A MET* 2.8 67.6 + - + +
26A ARG* 3.6 38.4 - - + +
40A VAL* 3.8 16.4 - - + +
41A ALA* 1.3 80.1 - - - +
43A PHE* 1.3 71.4 + - - +
79A ARG* 4.1 22.4 - - - +
80A ILE 3.4 7.2 - - - +
81A GLU* 3.9 23.8 - - + +
110A PHE* 3.5 7.8 - - - -
17B G 6.3 0.2 - - - +
18B A 6.2 1.1 - - - +
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Residues in contact with PHE 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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17A ILE* 3.8 35.7 - - + -
21A GLY* 5.1 1.1 - - - -
22A SER 3.6 4.9 - - - -
23A PHE* 3.4 37.7 - + - -
42A ILE* 1.3 72.5 - - - +
44A SER* 1.4 61.3 + - - +
45A VAL* 3.9 17.3 - - + -
62A PHE* 4.5 10.5 - + - -
78A TYR* 4.3 17.0 - + - -
79A ARG* 3.2 6.2 - - - +
80A ILE* 2.9 41.9 + - + +
86A LEU* 3.7 22.4 - - + +
90A ILE* 4.1 22.9 - - + -
94A PHE* 4.3 11.0 - + - -
110A PHE* 4.4 6.3 - - + -
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Residues in contact with SER 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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20A GLU 4.4 0.2 - - - +
21A GLY* 3.9 0.2 - - - -
22A SER* 2.8 40.5 + - - -
24A MET* 3.5 22.4 - - - -
43A PHE* 1.4 75.7 - - - +
45A VAL* 1.3 66.4 + - - +
46A THR* 3.6 11.5 + - - -
78A TYR 3.4 5.6 - - - -
79A ARG* 2.6 38.6 + - - +
16B G 4.9 1.7 + - - -
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Residues in contact with VAL 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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16A PHE* 3.9 27.8 - - + -
17A ILE* 3.6 26.7 - - + -
20A GLU* 4.7 11.2 - - + -
21A GLY* 4.6 0.9 - - - -
43A PHE* 3.9 18.4 - - + -
44A SER* 1.3 77.6 + - - +
46A THR* 1.3 61.7 + - - +
47A VAL* 4.3 4.9 - - + -
55A LEU* 4.1 20.5 - - + +
58A LEU* 4.2 11.2 - - + -
76A PHE 3.9 0.5 - - - +
77A SER* 3.1 3.1 - - - -
78A TYR* 2.7 44.2 + - + +
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Residues in contact with THR 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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20A GLU* 3.8 9.2 + - - +
44A SER* 3.6 9.6 + - - -
45A VAL* 1.3 78.6 + - - +
47A VAL* 1.3 67.5 + - - +
71A SER* 4.1 15.6 + - - +
75A THR* 4.0 20.2 - - + +
76A PHE 3.4 11.2 - - - +
77A SER* 3.5 12.1 - - - -
79A ARG* 4.8 3.3 + - - -
14B A 3.5 24.4 - - + +
15B T 3.6 35.5 + - + +
16B G 4.9 0.9 + - - -
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Residues in contact with VAL 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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16A PHE* 4.5 15.0 - - + -
20A GLU* 3.8 15.9 - - - +
45A VAL* 4.6 2.5 - - + -
46A THR* 1.3 81.3 - - - +
48A ASP* 1.3 72.2 + - - +
51A ASP* 3.6 23.8 - - + +
52A LEU* 5.0 0.2 - - - -
54A LEU* 5.6 1.3 - - + -
55A LEU* 3.7 37.7 - - + -
75A THR* 3.2 7.9 - - - -
76A PHE* 2.9 29.3 + - + +
403A MXE 4.6 3.1 - - - +
14B A 3.5 11.9 - - - +
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Residues in contact with ASP 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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47A VAL* 1.3 82.9 - - - +
49A LYS* 1.3 59.1 + - - +
50A LYS* 3.0 49.0 + - + +
51A ASP* 2.7 27.9 + - - +
74A SER* 3.2 27.8 + - - +
75A THR* 4.0 5.9 - - - +
13B A 4.1 25.3 + - + +
14B A 2.9 17.9 + - - +
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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