Contacts of the strand formed by residues 18 - 26 (chain D) in PDB entry 2MF1
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 ILE 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ILE* 4.4 26.9 - - + -
18C ILE* 6.2 2.7 - - + -
48C TYR* 5.9 0.2 - - - -
13D ASN* 3.6 6.6 + - - +
14D ILE* 3.0 60.1 + - + +
15D GLY* 4.8 4.0 - - - +
16D ASP 3.9 0.4 - - - -
17D ASP* 1.3 91.8 + - + +
19D THR* 1.3 76.1 + - - +
20D ILE* 4.4 4.0 - - + -
34D ILE* 4.5 1.3 - - + -
35D ASN 3.4 9.2 - - - +
36D ALA* 3.8 22.9 - - + -
37D PRO* 4.6 2.2 - - + -
40D VAL* 4.6 14.4 - - + -
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Residues in contact with THR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLU* 6.1 1.1 - - + -
11D SER* 5.1 6.5 - - - -
12D ILE 3.6 11.2 - - - +
13D ASN* 3.1 19.9 + - - +
17D ASP 5.1 1.7 + - - -
18D ILE* 1.3 73.2 - - - +
20D ILE* 1.3 78.4 + - - +
21D THR* 4.5 7.4 - - - +
34D ILE 3.7 0.3 - - - -
35D ASN* 2.8 51.6 + - + +
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 4.0 16.2 - - + -
20C ILE* 5.7 7.6 - - + -
32C ILE* 6.0 5.2 - - + -
34C ILE* 6.3 0.7 - - + -
11D SER* 3.3 4.0 - - - -
12D ILE* 2.8 55.1 + - + +
14D ILE* 4.2 21.1 - - + -
18D ILE* 4.4 3.4 - - + -
19D THR* 1.3 83.4 - - - +
21D THR* 1.3 70.1 + - - +
22D ILE 5.0 0.7 - - - +
32D ILE* 3.8 19.5 - - + -
33D GLY 3.4 9.2 - - - +
34D ILE* 3.6 30.7 - - + -
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Residues in contact with THR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.5 13.9 - - - +
9D GLY* 4.7 6.5 - - - +
10D GLU 3.5 15.3 - - - +
11D SER* 3.7 13.3 + - - +
19D THR* 4.5 7.1 - - - +
20D ILE* 1.3 77.8 + - - +
22D ILE* 1.3 62.3 + - - +
23D LEU* 3.3 25.1 + - + +
32D ILE* 3.6 4.7 - - - -
33D GLY 2.8 39.0 + - - +
11G U 4.6 15.9 + - + +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.2 14.1 - - + -
32C ILE* 4.9 13.2 - - + -
6D ARG* 4.7 10.1 - - + +
7D LYS 3.1 24.7 - - - +
8D VAL* 3.9 17.3 - - + -
9D GLY* 2.8 34.0 + - - -
10D GLU* 3.0 19.0 + - + +
12D ILE* 6.0 2.7 - - + +
20D ILE* 5.0 1.4 - - + +
21D THR* 1.3 69.4 - - - +
23D LEU* 1.3 56.4 + - - +
24D GLY 3.5 15.5 - - - +
30D VAL* 3.2 35.7 - - + -
31D ARG 3.6 7.4 - - - +
32D ILE* 4.4 7.8 - - + +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.4 4.5 - - + -
3C ILE* 3.4 41.7 - - + -
8D VAL* 4.9 0.3 - - - +
9D GLY* 4.5 6.9 + - - -
21D THR* 3.7 29.4 - - + +
22D ILE* 1.3 72.5 - - - +
24D GLY* 1.3 57.8 + - - +
31D ARG* 2.8 28.7 + - - +
32D ILE 4.1 0.4 - - - -
33D GLY* 3.5 18.8 - - - +
11G U 3.7 32.8 - - + +
12G A 5.0 1.1 - - + -
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Residues in contact with GLY 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.6 19.7 - - - -
22D ILE* 3.4 8.8 - - - +
23D LEU* 1.3 79.9 - - - +
25D VAL* 1.3 61.3 + - - -
30D VAL* 3.6 1.0 - - - -
31D ARG* 2.8 36.4 + - - +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 4.2 17.7 - - + -
27C GLY 5.2 4.9 - - - +
28C GLN* 4.1 22.0 - - - +
29C GLN 5.6 0.2 - - - +
30C VAL* 4.2 17.5 - - + -
8D VAL* 3.7 17.8 - - + +
24D GLY* 1.3 79.8 - - - +
26D SER* 1.3 69.1 + - - +
27D GLY 4.4 11.9 - - - +
29D GLN 3.3 13.0 - - - +
30D VAL* 4.4 2.7 - - + +
31D ARG* 5.3 1.8 - - - -
2G G 4.8 4.6 + - - +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 1.3 76.6 + - - +
27D GLY* 1.3 58.1 + - - +
29D GLN* 2.8 41.8 + - - +
31D ARG* 4.3 18.6 + - - +
2G G 3.6 24.7 - - - -
3G U 3.1 21.8 + - - -
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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