Contacts of the strand formed by residues 3 - 14 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1I GLY* 3.1 25.6 + - - -
2I PRO* 1.3 84.3 + - - +
4I SER* 1.3 66.0 + - - +
29I ASP* 2.7 33.2 + - - +
102I GLU* 3.6 2.8 - - - +
103I VAL* 2.9 34.8 + - + +
168I LEU* 4.0 7.4 - - + -
172I LEU* 4.0 31.5 - - + +
180I LEU* 4.3 29.8 - - + +
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Residues in contact with SER 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I HIS* 1.3 78.5 - - - +
5I LEU* 1.3 61.9 + - - +
6I ARG* 4.5 11.5 + - - +
27I TYR 4.8 1.4 + - - -
28I VAL* 3.7 2.6 - - - +
29I ASP* 2.8 32.2 + - - +
30I ASP* 4.8 2.4 + - - -
101I CYS 2.9 20.6 - - - -
102I GLU* 4.0 13.5 - - - -
113I TYR* 4.7 4.9 - - - -
168I LEU* 2.8 26.8 - - - +
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Residues in contact with LEU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I SER* 1.3 78.2 - - - +
6I ARG* 1.3 62.0 + - - +
7I TYR* 4.4 15.4 - - + -
27I TYR 3.7 2.2 - - - -
28I VAL* 3.3 33.0 - - + +
33I PHE* 3.8 9.0 - - + -
100I GLY* 2.9 22.2 - - - -
101I CYS* 2.9 13.5 + - - -
164I CYS* 3.7 20.7 - - - +
167I TRP* 4.1 5.2 - - + -
168I LEU* 3.6 32.8 - - + +
171I TYR* 3.3 26.5 - - + -
1Q GLU 4.3 7.4 - - - +
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Residues in contact with ARG 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I SER* 4.5 11.8 + - - +
5I LEU* 1.3 77.4 - - - +
7I TYR* 1.3 64.9 + - - +
8I PHE* 3.7 27.5 - - + -
26I GLY* 3.5 3.1 - - - -
27I TYR* 2.6 46.5 + - + +
30I ASP* 3.9 28.0 + - - +
98I ILE* 6.0 3.8 - - + -
99I SER 3.4 7.9 - - - +
102I GLU* 4.9 8.7 + - - -
113I TYR* 2.9 40.1 + - + +
58M LYS* 3.1 47.8 - - - +
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Residues in contact with TYR 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.4 15.3 - - + -
6I ARG* 1.3 77.3 - - - +
8I PHE* 1.3 59.1 + - - +
9I VAL* 3.9 4.0 + - + -
24I GLU* 4.3 5.4 - - - -
25I VAL 3.8 4.9 - - - -
26I GLY* 3.4 28.0 - - - -
33I PHE* 4.1 11.1 - + - -
34I VAL* 4.3 9.5 - - + +
45I TYR* 4.3 11.8 - + - -
63I GLU* 4.8 1.9 + - - -
97I VAL* 2.4 25.3 - - - +
99I SER* 2.6 30.8 + - - +
100I GLY* 5.8 0.4 - - - -
159I TYR* 3.3 9.6 - - - -
164I CYS* 6.2 0.4 - - - -
171I TYR* 3.6 14.6 + - - -
1Q GLU* 3.3 32.8 - - - -
2Q GLN* 3.2 43.2 + - + +
5Q PHE* 5.2 0.7 - - + -
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Residues in contact with PHE 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ARG* 3.7 35.0 - - + -
7I TYR* 1.3 78.0 - - - +
9I VAL* 1.3 62.5 + - - +
10I THR* 4.2 1.4 + - - +
23I MET 4.2 0.9 - - - +
24I GLU* 4.0 1.7 - - - -
25I VAL* 3.0 50.4 + - + +
27I TYR* 3.0 30.7 - + + -
97I VAL 3.3 3.6 - - - -
98I ILE* 3.3 24.0 - - + -
56M PHE* 3.3 42.1 - + + +
57M SER 3.2 24.5 - - - -
58M LYS* 4.2 17.0 - - + -
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Residues in contact with VAL 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I TYR* 4.8 2.5 - - + -
8I PHE* 1.3 79.6 - - - +
10I THR* 1.3 67.1 + - - +
22I TYR* 3.4 23.8 - - + +
23I MET 4.0 4.7 - - - +
24I GLU* 3.9 15.0 - - + +
74I PHE* 3.3 29.2 - - + -
95I ILE 3.5 0.2 - - - +
96I GLN* 3.0 8.0 - - - +
97I VAL* 2.8 48.7 + - + +
56M PHE* 4.3 0.7 - - - -
2Q GLN* 3.3 26.9 - - - +
5Q PHE* 4.4 6.3 - - + -
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Residues in contact with THR 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I PHE 5.5 1.3 - - - +
9I VAL* 1.3 81.1 - - - +
11I ALA* 1.3 63.4 + - - +
12I VAL* 5.0 1.2 + - - +
21I ARG* 3.4 8.7 - - - +
22I TYR* 3.6 2.4 - - - -
23I MET* 2.9 56.7 + - + +
94I THR* 4.0 5.9 - - - +
95I ILE 3.0 10.9 + - - -
96I GLN* 4.9 0.2 - - - -
54M MET* 5.7 1.1 - - + +
56M PHE* 4.8 9.6 - - + -
62M PHE* 3.9 28.1 - - + -
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 5.1 0.2 - - - +
10I THR* 1.3 76.1 + - - +
12I VAL* 1.3 58.5 + - - +
20I PRO* 4.8 8.5 - - + -
21I ARG 3.0 10.1 - - - +
22I TYR* 3.9 17.0 - - + -
74I PHE* 4.1 12.1 - - + -
94I THR 3.2 0.2 - - - -
95I ILE* 2.7 67.9 + - + +
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Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I THR* 5.4 1.8 - - - +
11I ALA* 1.3 75.0 - - - +
13I SER* 1.3 63.7 + - - +
14I ARG* 3.7 9.2 + - + +
20I PRO* 3.1 3.3 - - - +
21I ARG* 2.9 44.3 + - + +
92I SER* 3.3 18.4 - - - +
93I HIS* 2.9 18.6 - - - +
94I THR* 3.0 24.9 - - + +
33M PRO* 4.6 11.7 - - + -
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Residues in contact with SER 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I VAL* 1.3 72.7 - - - +
14I ARG* 1.3 60.8 + - - +
15I PRO* 3.3 12.8 - - - +
20I PRO* 3.9 8.5 - - - -
78I LEU* 3.4 26.4 - - - +
82I LEU* 5.5 4.8 - - - +
91I GLY 4.2 0.9 + - - -
92I SER* 2.4 34.5 + - - -
93I HIS* 2.6 45.0 + - - +
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Residues in contact with ARG 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.8 12.6 + - + +
13I SER* 1.3 79.0 - - - +
15I PRO* 1.3 56.8 - - - +
17I LEU* 2.8 50.2 + - + -
18I GLY 2.9 16.8 + - - +
19I GLU 3.8 19.8 + - - +
20I PRO* 4.3 2.2 - - - +
21I ARG* 2.9 50.9 - - - +
39I ASP* 2.8 33.7 + - - -
92I SER* 4.7 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