Contacts of the strand formed by residues 25 - 34 (chain k) in PDB entry 5MQF
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 ARG 25 (chain k).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20k LYS* 3.6 1.4 - - - -
21k LEU* 2.7 45.0 + - + +
22k ASN 3.6 15.3 - - - +
23k GLY* 3.2 3.6 - - - +
24k GLY* 1.3 78.0 - - - +
26k HIS* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19k LEU 3.3 11.0 - - - +
20k LYS* 4.9 3.6 - - + -
21k LEU* 5.5 0.2 - - - -
24k GLY 4.0 2.3 + - - +
25k ARG* 1.3 77.4 - - - +
27k VAL* 1.3 60.9 + - - +
47k GLU* 4.0 1.6 - - - -
48k MET* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18k SER* 3.7 1.2 - - - -
19k LEU* 2.8 42.7 + - + +
21k LEU* 6.1 0.4 - - - +
26k HIS* 1.3 75.5 - - - +
28k GLN* 1.3 60.4 + - - +
45k CYS* 5.5 5.4 - - + -
46k VAL 3.3 17.9 - - - +
47k GLU* 4.6 3.6 - - - -
48k MET* 4.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17k LEU 3.2 13.9 - - - +
18k SER* 4.7 5.2 - - - -
19k LEU* 5.7 0.2 - - - -
27k VAL* 1.3 75.3 - - - +
29k GLY* 1.3 58.0 + - - +
44k GLU 3.7 2.3 - - - +
45k CYS* 3.3 3.8 - - - -
46k VAL* 2.9 41.0 + - + +
48k MET* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16k LYS* 4.3 5.3 - - - +
17k LEU* 2.9 36.3 + - - +
28k GLN* 1.3 74.3 - - - +
30k ILE* 1.3 62.4 + - - -
31k LEU 3.8 0.2 + - - -
42k ILE* 4.9 10.4 - - - +
43k ASP 3.5 10.8 - - - -
44k GLU* 4.1 4.9 - - - -
45k CYS* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14k ASP* 4.9 7.2 - - - -
15k LYS 3.3 15.5 - - - +
16k LYS* 4.3 2.7 - - + +
29k GLY* 1.3 71.4 - - - -
31k LEU* 1.3 66.5 + - - +
32k ARG* 3.2 1.4 + - - +
42k ILE* 3.5 2.8 - - - -
43k ASP* 2.9 49.1 + - + +
44k GLU* 5.3 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12k PHE* 3.6 28.5 - - + +
13k MET* 4.0 3.9 - - - +
14k ASP* 2.7 31.6 + - - +
15k LYS 3.1 10.5 + - - +
17k LEU* 5.7 5.6 - - + -
29k GLY 3.8 2.4 + - - -
30k ILE* 1.3 68.6 - - - +
32k ARG* 1.3 59.6 + - - +
33k GLY 3.6 4.0 - - - +
40k LEU* 6.6 0.2 - - + -
41k VAL 3.8 6.1 - - - +
42k ILE* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14j MET* 3.6 8.5 - - - +
15j VAL* 2.8 34.4 + - + -
13k MET* 6.2 2.2 - - - -
30k ILE 3.2 5.5 + - - +
31k LEU* 1.3 73.7 - - - +
33k GLY* 1.3 57.3 + - - +
41k VAL* 2.8 24.2 + - + +
42k ILE 5.3 0.2 - - - -
43k ASP* 4.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14j MET* 4.9 6.7 - - - -
15j VAL 3.0 17.3 - - - -
17j PRO* 4.1 0.9 - - - -
13k MET* 6.3 0.2 - - - +
31k LEU* 3.6 4.6 - - - +
32k ARG* 1.3 82.2 - - - +
34k PHE* 1.3 64.2 + - - +
40k LEU* 3.4 4.5 - - - +
41k VAL* 2.8 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15j VAL 3.9 0.8 + - - -
16j GLN* 4.8 5.9 - - - +
17j PRO* 3.8 11.2 - - - +
7k PRO* 5.8 4.3 - - + -
9k LEU* 5.1 15.3 - - + -
33k GLY* 1.3 76.3 - - - +
35k ASP* 1.3 66.6 + - - +
38k MET* 5.3 4.0 - - - -
39k ASN 3.2 15.7 - - - +
40k LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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