Contacts of the strand formed by residues 24 - 33 (chain E) in PDB entry 3MQT
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 GLU 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E VAL 4.0 0.2 - - - +
16E ASN* 3.9 2.0 + - - +
17E VAL* 3.1 44.2 + - + +
23E SER* 1.3 74.3 - - - +
25E ASN* 1.3 61.5 + - - +
312E LYS 5.6 1.2 - - - +
341E TRP* 4.2 9.2 + - - -
343E GLY* 3.4 19.2 - - - -
344E THR* 3.2 28.3 + - - +
345E LEU* 3.2 44.4 + - + +
346E THR* 4.2 4.5 + - - -
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Residues in contact with ASN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL 2.9 19.1 - - - +
16E ASN* 3.6 22.4 + - - +
23E SER* 3.8 12.3 + - - -
24E GLU* 1.3 76.9 - - - +
26E THR* 1.3 61.4 + - - +
45E GLY 4.7 3.1 - - - +
47E PRO* 3.6 21.5 - - + +
312E LYS* 3.4 16.5 + - - +
345E LEU* 3.6 11.1 - - - +
59H GLU* 3.5 38.7 + - - +
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Residues in contact with THR 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E PRO* 3.8 0.2 - - - +
15E VAL* 2.9 44.8 + - + +
25E ASN* 1.3 78.2 - - - +
27E VAL* 1.3 71.1 + - - +
28E ILE* 4.3 9.9 - - + -
42E GLU* 2.7 36.3 + - - +
43E ALA 4.2 0.7 + - - -
45E GLY 5.7 0.7 - - - -
47E PRO* 3.9 4.1 - - - +
312E LYS* 3.6 19.4 + - - +
313E THR* 4.0 13.7 - - - +
345E LEU* 4.1 5.4 - - + -
349E LEU* 4.2 11.4 - - + -
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.7 42.0 - - + -
13E ILE 3.6 9.9 - - - +
14E PRO* 4.5 1.6 - - + -
26E THR* 1.3 79.8 + - - +
28E ILE* 1.3 64.3 + - - +
29E VAL* 4.2 1.7 - - + +
42E GLU* 3.2 7.1 - - - +
43E ALA* 3.1 37.6 + - + +
45E GLY 4.3 3.4 - - - +
47E PRO* 3.3 40.8 - - + +
50E MET* 3.8 16.2 - - + -
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Residues in contact with ILE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLU 3.3 2.6 - - - +
12E PHE* 3.4 2.3 - - - -
13E ILE* 2.6 57.9 + - + +
15E VAL* 3.8 26.7 - - + -
26E THR* 4.3 7.6 - - + -
27E VAL* 1.3 71.9 - - - +
29E VAL* 1.3 63.9 + - - +
30E LYS 4.6 0.2 - - - +
40E LEU* 4.0 26.2 - - + -
41E GLY 3.6 7.0 - - - +
42E GLU* 4.6 0.2 - - - +
315E ILE* 3.8 21.1 - - + -
349E LEU* 4.3 9.9 - - + -
373E LEU* 4.6 6.1 - - + -
378E VAL* 4.2 27.8 - - + -
386E PHE* 5.1 3.4 - - + -
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Residues in contact with VAL 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 4.2 8.1 - - + -
11E GLU 3.3 4.3 - - - +
12E PHE* 4.0 33.2 - - + -
27E VAL* 4.2 8.7 - - + +
28E ILE* 1.3 78.0 - - - +
30E LYS* 1.3 61.9 + - - +
31E VAL* 4.2 7.0 - - + -
39E GLY 3.4 1.4 - - - +
40E LEU* 3.4 7.1 - - - +
41E GLY 2.8 37.4 + - - +
43E ALA* 4.3 4.7 - - + +
104E GLY* 3.7 37.5 - - - +
105E ILE* 3.9 23.1 - - + -
108E ALA* 3.6 1.1 - - + +
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E SER* 3.9 1.4 + - - +
10E VAL* 3.4 2.8 - - - -
11E GLU* 2.8 53.1 + - + +
13E ILE* 4.2 17.0 - - + -
28E ILE* 5.0 0.2 - - + -
29E VAL* 1.3 72.0 - - - +
31E VAL* 1.3 63.5 + - - +
32E THR* 3.9 18.1 + - - +
38E TYR* 3.7 37.6 - - + -
39E GLY 3.5 3.8 - - - -
40E LEU* 4.3 5.6 - - + -
386E PHE* 3.4 58.3 + - + -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 3.6 39.3 - - + -
9E SER 3.4 4.0 - - - +
10E VAL* 4.3 9.2 - - + -
29E VAL* 4.2 11.0 - - + -
30E LYS* 1.3 78.7 - - - +
32E THR* 1.3 60.2 + - - +
38E TYR* 3.0 3.3 - - - -
39E GLY 2.7 36.6 + - - +
105E ILE* 4.2 10.3 - - + -
108E ALA* 3.6 23.8 - - + +
109E LEU* 3.8 21.8 - - + -
112E LEU* 3.8 10.3 - - + +
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Residues in contact with THR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 3.7 3.5 - - - -
8E VAL* 2.8 28.3 + - + -
9E SER* 3.0 29.0 + - - +
30E LYS* 3.9 18.2 + - - +
31E VAL* 1.3 75.6 - - - +
33E ASP* 1.3 71.5 + - - +
36E GLY* 3.9 18.4 - - - +
37E VAL 3.3 11.7 - - - +
38E TYR* 3.8 10.4 - - + +
112E LEU* 4.7 1.6 - - - -
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Residues in contact with ASP 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ALA* 4.1 7.7 - - - +
6E ASN 3.3 16.4 - - - +
7E ILE* 4.2 0.9 - - - +
8E VAL* 4.0 8.8 - - - +
31E VAL 4.3 0.4 + - - -
32E THR* 1.3 80.9 - - - +
34E GLU* 1.3 60.7 + - - +
35E ASN* 2.9 18.4 + - - +
36E GLY* 3.1 11.4 + - - -
37E VAL* 2.8 49.4 + - - +
112E LEU* 4.3 8.4 - - + +
116E GLN* 2.8 36.5 + - - +
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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