Contacts of the strand formed by residues 3 - 14 (chain H) in PDB entry 1MWA
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 HIS 3 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLY* 3.0 35.5 + - - -
2H PRO* 1.3 74.8 + - - +
4H SER* 1.3 59.2 + - - +
29H ASP* 2.8 34.2 + - - +
102H GLU* 3.3 3.8 - - - +
103H VAL* 2.8 36.7 + - + +
104H GLY 4.9 5.2 - - - -
105H SER* 5.6 1.7 - - - -
168H LEU* 3.7 16.9 - - + +
172H LEU* 3.4 32.4 - - + +
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Residues in contact with SER 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H HIS* 1.3 75.2 - - - +
5H LEU* 1.3 59.6 + - - +
6H ARG* 2.8 48.6 + - - +
27H TYR 4.2 0.4 + - - -
28H VAL* 3.4 1.4 - - - -
29H ASP* 2.9 40.0 + - - +
30H ASP* 4.4 0.7 + - - -
101H CYS 3.0 13.2 - - - -
102H GLU* 4.0 6.5 - - - -
168H LEU* 3.3 13.5 - - - +
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Residues in contact with LEU 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H SER* 1.3 73.0 - - - +
6H ARG* 1.3 67.2 + - - +
7H TYR* 3.9 18.8 - - + +
27H TYR 3.4 6.1 - - - +
28H VAL* 4.3 2.2 - - + -
33H PHE* 3.7 30.5 - - + -
100H GLY* 3.0 3.9 - - - -
101H CYS* 2.8 34.2 + - - -
164H CYS* 3.2 44.2 - - - +
167H TRP* 4.3 10.5 - - + -
168H LEU* 3.8 26.9 - - + +
171H TYR* 4.2 5.4 - - + -
1P GLU 4.5 7.0 - - - +
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Residues in contact with ARG 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H SER* 2.8 30.0 + - - +
5H LEU* 1.3 79.6 - - - +
7H TYR* 1.3 64.9 + - - +
8H PHE* 4.0 26.2 - - + -
26H GLY* 3.3 1.0 - - - -
27H TYR* 2.6 50.2 + - + +
30H ASP* 3.7 27.1 + - - +
98H ILE* 4.9 2.2 - - + -
99H SER 3.3 9.4 - - - +
100H GLY* 4.5 0.2 - - - -
102H GLU* 2.5 29.1 + - - +
113H TYR* 2.4 50.6 + - + +
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Residues in contact with TYR 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 3.9 22.2 - - + +
6H ARG* 1.3 74.6 - - - +
8H PHE* 1.3 63.3 + - - +
9H VAL* 3.9 4.5 + - + +
24H GLU* 4.7 0.4 - - - +
25H VAL 3.2 6.3 - - - +
26H GLY* 3.5 14.8 - - - -
33H PHE* 3.9 13.5 - + - -
34H VAL* 3.8 17.7 - - + -
45H TYR* 3.6 26.4 - + - -
59H TYR* 4.5 2.8 + - - -
63H GLU* 4.8 0.2 + - - -
97H VAL 3.6 2.4 - - - +
98H ILE* 3.5 3.6 - - - -
99H SER* 2.8 40.6 + - - +
159H TYR* 3.6 9.0 - - - -
164H CYS* 6.4 0.2 - - - -
171H TYR* 3.9 2.1 + - - -
1P GLU* 3.1 46.8 + - - -
2P GLN* 3.5 36.6 - - - +
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Residues in contact with PHE 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 4.0 19.7 - - + -
7H TYR* 1.3 79.7 - - - +
9H VAL* 1.3 60.5 + - - +
10H THR* 4.2 0.9 + - - -
23H MET 3.8 1.4 - - - +
24H GLU* 3.6 2.6 - - - -
25H VAL* 2.6 42.9 + - + +
27H TYR* 3.5 38.1 - + + +
97H VAL 3.6 3.8 - - - -
98H ILE* 3.9 35.0 - - + -
56L PHE* 3.4 55.5 - + + -
57L SER* 4.3 7.2 - - - -
58L LYS* 4.6 4.0 - - + -
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Residues in contact with VAL 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 4.4 7.6 - - + +
8H PHE* 1.3 75.9 - - - +
10H THR* 1.3 66.5 + - - +
22H TYR* 3.9 30.3 - - + +
23H MET 3.6 4.3 - - - +
24H GLU* 4.4 8.7 - - + -
74H PHE* 3.9 13.5 - - + -
95H ILE 3.5 0.3 - - - +
96H GLN* 3.0 8.5 - - - +
97H VAL* 2.8 61.7 + - + +
56L PHE* 3.9 1.3 - - - -
2P GLN* 3.6 24.0 - - - +
5P PHE* 4.3 9.4 - - + -
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Residues in contact with THR 10 (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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8H PHE 4.8 0.7 + - - -
9H VAL* 1.3 75.1 - - - +
11H ALA* 1.3 64.1 + - - +
12H VAL* 4.0 17.0 - - + -
21H ARG 3.8 1.2 - - - +
22H TYR* 3.5 6.1 - - - -
23H MET* 3.0 46.0 + - - +
94H THR* 4.2 0.7 - - + -
95H ILE 3.3 7.2 - - - +
96H GLN* 4.2 3.4 - - + -
33L PRO* 5.6 0.4 - - + -
56L PHE* 3.0 28.6 - - - -
62L PHE* 3.8 30.8 - - + -
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Residues in contact with ALA 11 (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 THR* 1.3 76.4 - - - +
12H VAL* 1.3 62.5 + - - +
13H SER 4.2 0.2 - - - -
20H PRO* 5.3 1.8 - - + -
21H ARG 3.5 7.4 - - - +
22H TYR* 4.3 7.4 - - + -
74H PHE* 4.1 34.5 - - + -
78H LEU* 4.0 19.4 - - + +
93H HIS 3.7 0.5 - - - +
94H THR* 3.3 2.9 - - - -
95H ILE* 2.9 36.4 + - + +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 4.0 12.1 - - + -
11H ALA* 1.3 78.4 - - - +
13H SER* 1.3 63.7 + - - +
14H ARG* 3.7 8.2 + - + +
20H PRO* 3.2 4.5 - - - +
21H ARG* 3.1 45.3 + - + +
92H SER* 4.8 5.2 - - - +
93H HIS 3.0 11.7 - - - +
94H THR* 3.2 24.0 - - + +
33L PRO* 3.8 22.7 - - + -
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Residues in contact with SER 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 1.3 72.9 - - - +
14H ARG* 1.3 58.7 + - - +
15H PRO* 3.5 6.3 - - - -
20H PRO* 3.9 13.2 - - - -
78H LEU* 4.1 23.1 - - - +
91H GLY 3.8 5.2 + - - -
92H SER* 2.7 34.8 + - - -
93H HIS* 2.9 28.2 + - - +
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 4.3 7.8 - - + +
13H SER* 1.3 74.7 - - - +
15H PRO* 1.3 63.7 - - - +
17H LEU* 2.8 65.8 + - + +
18H GLY 2.9 17.8 + - - +
19H GLU 3.4 30.5 + - - +
20H PRO* 4.2 4.2 - - + +
21H ARG* 3.4 31.0 - - - +
39H ASP* 2.7 38.7 + - - -
92H SER* 4.8 1.3 - - - -
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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