Contacts of the strand formed by residues 24 - 33 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN* 4.3 0.7 - - - +
17H VAL* 3.0 45.7 + - + +
18H ALA 5.4 1.6 - - - +
23H SER* 1.3 78.0 - - - +
25H ASN* 1.3 64.1 + - - +
341H TRP* 4.9 3.2 + - - -
343H GLY* 3.5 13.8 - - - -
344H THR* 3.1 32.6 + - - -
345H LEU* 3.1 43.0 + - + +
346H THR* 4.0 3.5 + - - -
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Residues in contact with ASN 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLU* 3.4 38.8 + - - +
15H VAL 3.1 14.8 - - - +
16H ASN* 3.5 25.0 + - - +
23H SER* 4.0 1.8 - - - -
24H GLU* 1.3 80.4 - - - +
26H THR* 1.3 65.7 + - - +
45H GLY 4.8 1.9 - - - +
47H PRO* 3.7 22.4 - - + +
312H LYS* 3.4 16.8 + - - +
345H LEU* 3.6 11.0 - - - +
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Residues in contact with THR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PRO 3.8 0.2 - - - -
15H VAL* 2.8 48.2 + - + +
25H ASN* 1.3 80.2 - - - +
27H VAL* 1.3 70.5 + - - +
28H ILE* 4.4 5.8 - - + -
42H GLU* 2.7 37.7 + - - +
43H ALA 4.3 0.2 + - - -
45H GLY 5.6 0.4 - - - -
47H PRO* 3.7 8.1 - - - +
312H LYS* 3.6 18.4 + - - +
313H THR* 4.0 8.5 - - - +
345H LEU* 4.0 10.5 - - + -
349H LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PHE* 3.7 40.8 - - + -
13H ILE 3.6 12.1 - - - +
14H PRO* 4.7 1.1 - - + -
26H THR* 1.3 78.4 + - - +
28H ILE* 1.3 63.7 + - - +
29H VAL* 3.7 0.6 + - + -
42H GLU* 3.0 27.5 - - - +
43H ALA* 3.1 21.8 + - + +
45H GLY 4.1 4.3 - - - +
47H PRO* 3.5 34.1 - - + +
50H MET* 3.8 18.2 - - + -
51H LYS 5.3 0.2 - - - +
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Residues in contact with ILE 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H GLU 3.4 2.8 - - - +
12H PHE* 3.5 0.7 - - - -
13H ILE* 2.7 58.7 + - + +
15H VAL* 3.6 26.2 - - + -
26H THR* 4.4 6.1 - - + -
27H VAL* 1.3 72.6 - - - +
29H VAL* 1.3 70.9 + - - +
40H LEU* 4.1 19.3 - - + -
41H GLY 3.5 9.2 - - - +
42H GLU* 4.5 0.4 - - + +
315H ILE* 3.9 21.8 - - + -
349H LEU* 4.2 19.5 - - + -
373H LEU* 4.6 5.8 - - + -
378H VAL* 4.3 17.3 - - + -
386H PHE* 5.0 3.4 - - + -
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Residues in contact with VAL 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H VAL* 4.4 1.8 - - + -
11H GLU 3.3 7.2 - - - +
12H PHE* 4.0 31.0 - - + -
27H VAL 4.3 1.1 - - - +
28H ILE* 1.3 78.2 - - - +
30H LYS* 1.3 60.8 + - - +
31H VAL* 4.1 13.2 - - + -
39H GLY 3.6 1.0 - - - +
40H LEU* 3.3 5.9 - - - -
41H GLY 2.8 32.4 + - - +
43H ALA* 4.3 11.4 - - + +
104H GLY* 3.8 39.3 - - - +
105H ILE* 3.9 23.1 - - + -
108H ALA* 4.0 1.1 - - + +
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Residues in contact with LYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H SER* 3.9 1.7 + - - +
10H VAL* 3.5 2.1 - - - -
11H GLU* 2.9 47.3 + - + +
13H ILE* 4.3 17.5 - - + -
28H ILE* 3.9 0.6 + - + -
29H VAL* 1.3 73.4 - - - +
31H VAL* 1.3 64.2 + - - +
32H THR* 3.9 13.8 + - - +
38H TYR* 3.4 49.2 - - + -
39H GLY 3.4 3.1 - - - -
40H LEU* 4.1 7.4 - - + -
386H PHE* 3.8 44.7 + - + +
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ILE* 3.5 41.7 - - + -
9H SER 3.4 3.8 - - - +
10H VAL* 4.1 17.7 - - + -
29H VAL* 4.1 11.0 - - + -
30H LYS* 1.3 75.8 - - - +
32H THR* 1.3 59.4 + - - +
38H TYR* 3.0 3.1 - - - -
39H GLY 2.8 37.3 + - - +
105H ILE* 4.4 10.8 - - + -
108H ALA* 3.7 23.8 - - + +
109H LEU* 3.9 11.2 - - + -
112H LEU* 3.6 14.2 - - + +
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Residues in contact with THR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ILE* 3.7 3.5 - - - -
8H VAL* 2.8 26.5 + - + -
9H SER* 3.1 27.7 + - - +
30H LYS* 3.9 17.5 + - - +
31H VAL* 1.3 75.5 - - - +
33H ASP* 1.3 72.1 + - - +
36H GLY* 3.7 20.0 - - - +
37H VAL 3.3 10.3 - - - +
38H TYR* 3.8 10.2 - - + +
112H LEU* 4.6 1.6 - - - -
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Residues in contact with ASP 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H ALA* 4.1 9.1 - - + +
6H ASN 3.3 15.7 - - - +
7H ILE* 4.2 0.7 - - - +
8H VAL* 4.2 7.0 - - - +
31H VAL 4.3 0.2 + - - -
32H THR* 1.3 82.6 - - - +
34H GLU* 1.3 60.2 + - - +
35H ASN* 2.8 19.5 + - - +
36H GLY 2.9 15.9 + - - -
37H VAL* 2.8 45.6 + - - +
112H LEU* 3.9 8.2 - - + +
116H GLN* 2.9 36.9 + - - +
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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