Contacts of the strand formed by residues 36 - 44 (chain M) in PDB entry 1N9S
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 THR 36 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LYS* 3.9 2.8 - - - +
31M LEU* 3.2 50.4 + - + +
33M PHE* 4.3 1.0 + - - -
34M ASN* 3.7 18.5 + - - +
35M SER* 1.3 78.7 - - - +
37M GLU* 1.3 65.0 + - - +
38M TYR* 3.9 10.5 - - + +
58M GLU* 3.7 26.9 - - + +
59M PHE 3.1 10.5 - - - +
60M VAL* 4.2 10.7 - - + +
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Residues in contact with GLU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M GLY* 4.0 4.2 - - - -
29M VAL 3.1 24.5 - - - +
30M LYS* 4.2 14.7 - - + +
35M SER 3.9 1.1 + - - +
36M THR* 1.3 76.8 - - - +
38M TYR* 1.3 65.7 + - - +
39M ARG* 2.6 41.7 + - + -
57M GLU 3.8 0.5 - - - +
59M PHE* 2.8 41.0 + - + +
80M TYR* 4.9 5.7 + - - -
82M ARG* 2.8 39.6 + - - +
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Residues in contact with TYR 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L LYS* 5.9 0.5 - - - -
79L LEU* 3.5 15.3 - - + +
80L TYR* 3.4 29.4 - + - -
28M GLY* 3.6 0.5 - - - -
29M VAL* 2.7 49.3 + - + +
31M LEU* 3.6 30.5 - - + +
36M THR* 3.9 9.3 - - + +
37M GLU* 1.3 71.8 - - - +
39M ARG* 1.3 59.6 + - - +
53M LEU* 4.0 6.4 - - + +
56M ALA* 5.1 1.1 - - + -
57M GLU 3.7 4.0 - - - +
58M GLU* 3.0 51.3 + - + -
68M LEU* 4.0 15.7 - - + -
71M ILE* 4.0 19.3 - - + -
73M ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ARG* 4.8 9.3 + - - +
27M VAL 3.3 3.6 - - - -
28M GLY* 4.2 2.0 - - - -
37M GLU* 2.6 35.1 + - + +
38M TYR* 1.3 76.7 - - - +
40M GLY* 1.3 59.0 + - - +
53M LEU* 3.9 3.8 - - - -
55M GLU 3.5 1.7 - - - +
56M ALA* 3.0 4.2 - - - -
57M GLU* 2.7 37.0 + - + +
59M PHE* 3.1 57.2 - - + +
62M GLY* 4.6 12.5 + - - -
82M ARG* 3.6 13.0 - - - +
84M LEU* 3.7 26.7 - - + +
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Residues in contact with GLY 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ARG* 4.1 16.6 - - - +
27M VAL* 2.7 43.6 + - - +
39M ARG* 1.3 76.0 - - - +
41M THR* 1.3 59.2 + - - -
53M LEU* 3.9 8.3 - - - +
54M ASN 3.5 9.9 - - - -
55M GLU* 3.9 6.1 - - - -
84M LEU* 4.4 2.2 - - - +
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Residues in contact with THR 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ASN* 4.1 25.8 - - - +
25M HIS 3.5 13.9 - - - +
26M ARG* 4.4 6.2 + - - +
40M GLY* 1.3 73.1 - - - -
42M LEU* 1.3 64.7 - - - +
43M VAL* 3.1 7.1 + - + -
53M LEU* 3.4 4.1 - - - -
54M ASN* 2.7 54.3 + - + +
55M GLU* 4.5 9.9 + - - +
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Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M LEU* 4.4 13.5 - - + +
22M LEU* 3.9 36.8 - - + +
23M VAL* 3.5 5.8 - - - +
24M ASN* 2.6 33.2 + - - -
25M HIS 3.0 8.5 + - - -
27M VAL* 3.8 21.1 - - + -
40M GLY 3.6 1.2 + - - -
41M THR* 1.3 70.4 - - - +
43M VAL* 1.3 58.0 + - - +
44M SER 3.4 19.3 - - - +
45M THR* 3.5 17.0 - - + +
51M LEU* 3.7 20.0 - - + -
52M GLN 3.0 20.0 - - - +
53M LEU* 3.9 8.1 - - + -
81M ILE* 5.6 2.7 - - + -
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Residues in contact with VAL 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M VAL* 3.5 17.4 - - - +
24M ASN* 5.6 1.8 - - - +
41M THR* 3.1 7.4 + - + +
42M LEU* 1.3 73.6 - - - +
44M SER* 1.3 65.2 + - - +
52M GLN* 2.9 43.8 + - - +
54M ASN* 3.7 36.1 - - + +
70M GLU* 4.2 4.7 - - - +
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Residues in contact with SER 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE* 3.9 11.0 - - - -
23M VAL* 5.0 4.5 - - - -
42M LEU* 3.4 3.4 - - - +
43M VAL* 1.3 86.6 - - - +
45M THR* 1.3 71.6 + - - +
51M LEU* 3.3 1.4 - - - -
52M GLN* 2.8 57.5 + - - +
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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