Contacts of the strand formed by residues 36 - 45 (chain A) in PDB entry 3G33
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 PHE 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.1 13.5 - - + -
27A LYS* 3.9 32.8 - - + -
28A ALA 3.2 17.7 - - - +
29A ARG* 3.4 29.8 - - + -
34A GLY 5.1 4.9 - - - -
35A HIS* 1.3 78.6 - - - +
37A VAL* 1.3 62.0 + - - +
99A GLU* 5.0 0.2 - - - -
100A HIS* 3.1 43.4 + + + +
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Residues in contact with VAL 37 (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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11A TYR* 3.7 32.8 - - + -
26A TYR 3.6 0.3 - - - +
27A LYS* 3.7 2.6 - - - -
28A ALA* 2.8 52.1 + - + +
29A ARG 4.7 1.1 - - - -
30A ASP* 4.5 6.7 - - + +
35A HIS* 4.4 9.2 - - + +
36A PHE* 1.3 80.6 - - - +
38A ALA* 1.3 59.2 + - - +
39A LEU* 3.6 6.5 + - + -
80A MET* 5.0 10.8 - - + -
97A VAL* 3.7 22.7 - - + -
98A PHE 3.5 11.4 - - - +
99A GLU* 5.5 0.7 - - - -
100A HIS* 3.5 4.9 - - - -
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Residues in contact with ALA 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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17A ILE* 4.0 21.8 - - + -
25A VAL* 4.2 8.1 - - + -
26A TYR 3.5 5.4 - - - -
37A VAL* 1.3 69.2 - - - +
39A LEU* 1.3 65.7 + - - +
40A LYS* 3.4 2.8 + - - +
96A LEU 3.4 2.9 - - - +
98A PHE* 2.9 48.5 + - + +
99A GLU 4.8 1.1 - - - +
100A HIS* 3.5 15.3 - - + +
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Residues in contact with LEU 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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11A TYR* 4.4 18.2 - - + +
13A PRO* 4.8 11.9 - - + -
24A THR 4.2 1.4 - - - +
25A VAL* 3.5 6.4 - - - +
26A TYR* 2.7 55.4 + - + +
28A ALA* 3.8 28.0 - - + -
37A VAL* 3.6 6.3 + - + -
38A ALA* 1.3 69.8 - - - +
40A LYS* 1.3 59.8 + - - +
41A SER* 4.2 1.6 - - - +
83A CYS* 6.3 0.2 - - - -
95A THR* 3.9 16.6 - - + -
96A LEU 4.0 0.4 - - - -
97A VAL* 3.8 35.9 - - + -
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Residues in contact with LYS 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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22A TYR* 4.5 10.3 - - + +
24A THR 4.9 3.6 - - - +
25A VAL* 3.9 32.8 - - + +
38A ALA* 4.4 2.0 - - - +
39A LEU* 1.3 74.4 - - - +
41A SER* 1.3 60.7 + - - +
95A THR* 4.2 1.4 - - - +
96A LEU* 2.7 51.8 + - + +
98A PHE* 4.2 29.4 - - + +
162A ALA* 6.0 0.8 - - - +
163A ASP* 2.4 43.1 + - - +
166A LEU* 4.5 6.3 - - + +
170A TYR* 3.0 30.5 - - + +
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Residues in contact with SER 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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22A TYR 4.4 7.1 - - - +
24A THR 4.7 8.7 + - - +
26A TYR* 5.5 10.0 - - - -
39A LEU* 4.4 1.8 + - - +
40A LYS* 1.3 73.4 + - - +
42A VAL* 1.3 71.9 + - - +
93A LYS* 5.8 7.0 - - - -
94A VAL 3.4 7.0 - - - -
95A THR* 3.3 22.8 + - - +
170A TYR* 3.9 3.8 + - - -
173A GLN* 4.7 2.4 - - - +
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Residues in contact with VAL 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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41A SER* 1.3 76.9 - - - +
43A ARG* 1.3 56.1 + - - +
44A VAL* 3.8 6.9 + - + -
93A LYS* 3.5 3.8 - - - -
94A VAL* 2.7 60.0 + - + +
96A LEU* 4.1 9.9 - - + -
169A ILE* 4.0 20.4 - - + +
170A TYR* 2.3 53.2 - - + +
173A GLN* 3.2 18.4 - - - +
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Residues in contact with ARG 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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42A VAL* 1.3 72.4 - - - +
44A VAL* 1.3 60.1 + - - +
91A GLU* 3.7 34.3 + - - +
92A ILE 3.4 4.5 - - - +
93A LYS* 4.1 25.5 - - + +
172A TYR* 4.6 10.4 + - - +
173A GLN* 2.7 54.6 + - + +
174A MET 4.9 11.3 + - - +
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Residues in contact with VAL 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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42A VAL* 4.2 11.7 - - + +
43A ARG* 1.3 72.5 - - - +
45A PRO* 1.3 103.2 - - + +
54A LEU* 4.7 3.6 - - + -
55A PRO* 3.5 16.2 - - + -
58A THR* 4.3 20.4 - - + +
91A GLU* 2.9 11.4 - - - +
92A ILE* 2.4 57.2 + - + +
94A VAL* 3.4 29.4 - - + -
169A ILE* 5.3 2.0 - - + +
172A TYR* 5.9 0.9 - - + -
150D TRP* 6.2 1.6 - - + -
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Residues in contact with PRO 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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43A ARG 4.9 0.2 - - - +
44A VAL* 1.3 104.5 - - + +
46A ASN* 1.3 60.4 + - - +
47A GLY 5.2 4.7 - - - +
53A GLY 3.6 3.8 - - - +
54A LEU* 3.2 22.9 - - - +
55A PRO* 3.1 29.5 - - + +
58A THR* 5.0 0.9 - - - +
91A GLU* 4.6 3.4 - - + -
92A ILE* 4.5 0.6 - - - +
172A TYR* 4.3 26.7 - - + -
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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