Contacts of the strand formed by residues 8 - 17 (chain A) in PDB entry 2DMH
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 MET 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER 6.2 0.2 - - - +
7A GLY* 1.3 75.5 - - - +
9A LEU* 1.3 68.4 + - - +
10A ARG* 4.0 15.3 + - + +
58A GLU* 3.6 40.2 - - + +
59A PHE 3.1 20.2 - - - +
60A ASP* 4.4 12.8 - - + +
61A LEU* 3.3 6.4 - - - +
130A GLY 3.8 3.1 - - - +
132A ASP* 3.6 34.3 + - + +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 1.3 71.6 - - - +
10A ARG* 1.3 60.2 + - - +
11A VAL* 4.1 7.4 - - + -
35A PHE* 3.9 23.1 - - + -
58A GLU* 3.5 0.2 - - - -
59A PHE* 2.9 52.0 + - + +
61A LEU* 4.3 12.3 - - + +
66A LEU* 4.2 10.1 - - + -
72A LEU* 3.7 30.1 - - + -
95A LEU* 4.0 20.0 - - + -
129A ILE* 3.6 24.5 - - + -
130A GLY 3.6 9.6 - - - +
131A TYR* 4.2 12.6 - - + -
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 4.0 14.6 + - + +
9A LEU* 1.3 73.0 - - - +
11A VAL* 1.3 61.9 + - - +
12A ILE* 3.9 8.1 - - + -
56A ILE* 4.4 20.1 - - + +
57A LEU 3.1 12.1 - - - +
58A GLU* 3.8 30.2 + - + +
128A VAL 3.5 2.0 - - - +
129A ILE* 3.3 6.2 - - - +
130A GLY* 2.9 39.3 + - - +
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.1 9.4 - - + -
10A ARG* 1.3 76.0 - - - +
12A ILE* 1.3 65.1 + - - +
13A VAL* 3.7 3.5 + - + -
33A VAL* 4.2 8.7 - - + -
57A LEU* 2.8 59.7 + - + +
59A PHE* 3.9 20.6 - - + -
72A LEU* 3.5 41.3 - - + -
74A ILE* 5.0 0.9 - - + -
127A LEU* 4.8 7.4 - - + -
128A VAL 4.0 2.0 - - - -
129A ILE* 4.1 10.8 - - + +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 5.2 7.6 - - + -
11A VAL* 1.3 74.1 - - - +
13A VAL* 1.3 64.2 + - - +
14A GLU* 3.7 24.9 + - + +
54A ASN 5.5 0.7 - - - -
55A GLU 3.3 14.1 - - - +
56A ILE* 3.9 34.8 - - + +
127A LEU* 3.4 11.3 - - - +
128A VAL* 3.1 56.8 + - + +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.9 2.0 - - + +
12A ILE* 1.3 75.5 - - - +
14A GLU* 1.3 53.3 + - - +
15A SER 4.7 0.7 - - - +
31A VAL* 3.7 18.8 - - + -
33A VAL* 5.0 0.2 - - + -
42A THR* 3.7 22.7 - - + -
53A TRP* 3.5 34.3 - - + -
54A ASN* 2.7 35.4 + - - -
55A GLU* 2.9 17.1 + - + +
57A LEU* 3.7 21.1 - - + -
125A ILE* 4.6 2.0 - - + -
127A LEU* 3.6 22.7 - - + -
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.7 21.9 + - + +
13A VAL* 1.3 70.6 - - - +
15A SER* 1.3 71.4 + - - +
52A VAL* 3.9 1.9 - - - +
53A TRP 3.3 3.0 + - - -
54A ASN* 2.7 39.0 + - - +
109A LYS* 5.8 4.9 - - - +
126A ASP* 3.5 31.9 + - + +
128A VAL* 5.1 12.8 - - + -
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.8 0.8 - - - +
14A GLU* 1.3 86.7 - - - +
16A ALA* 1.3 64.0 + - - +
17A SER* 5.4 1.0 + - - -
51A PRO 3.0 17.5 - - - -
52A VAL* 3.6 20.3 - - - +
53A TRP* 3.9 11.4 - - - -
125A ILE* 3.6 2.2 - - - +
126A ASP* 3.2 36.3 + - - +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 1.3 77.1 - - - +
17A SER* 1.3 70.7 + - - +
19A ILE* 4.3 9.9 - - + -
49A LEU 4.7 0.2 - - - -
50A ASN* 3.0 22.9 - - - +
51A PRO* 3.0 16.1 + - + +
53A TRP* 3.7 22.8 - - + -
76A VAL* 6.1 2.2 - - + -
113A LEU* 5.8 3.6 - - + -
123A ALA* 6.5 0.2 - - + -
124A THR 3.5 11.4 - - - +
125A ILE* 4.1 11.9 - - + +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 5.4 1.2 + - - -
16A ALA* 1.3 80.5 + - - +
18A ASN* 1.3 84.7 + - - +
19A ILE* 3.3 4.7 + - - +
49A LEU 4.5 0.4 - - - -
50A ASN* 3.2 28.1 + - - +
123A ALA* 3.6 1.7 - - - +
124A THR* 2.9 31.1 + - - +
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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