Contacts of the strand formed by residues 7 - 16 (chain B) in PDB entry 3MQT
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 7 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN* 1.3 73.0 - - - +
8B VAL* 1.3 64.6 + - - +
9B SER 3.8 10.8 - - - +
10B VAL* 4.5 2.2 - - + -
31B VAL* 3.7 24.7 - - + -
32B THR 3.7 6.5 - - - +
33B ASP* 4.2 1.1 - - - +
34B GLU* 5.3 0.5 - - - +
70B VAL* 3.4 36.3 - - + +
71B ILE* 3.8 12.2 - - + +
72B GLY* 2.8 27.9 + - - -
73B ARG* 2.9 20.6 + - + +
75B PRO* 4.1 14.4 - - + -
81B ASN* 5.1 0.9 - - - +
109B LEU* 3.8 28.3 - - + -
112B LEU* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN 3.6 0.6 + - - -
7B ILE* 1.3 75.0 - - - +
9B SER* 1.3 67.8 + - - +
32B THR* 2.7 16.8 + - + +
33B ASP 4.0 7.9 - - - +
34B GLU* 3.4 41.5 - - + +
71B ILE* 3.7 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 0.9 - - - +
8B VAL* 1.3 86.4 - - - +
10B VAL* 1.3 70.0 + - - +
11B GLU* 5.3 5.7 + - - +
30B LYS 4.4 0.8 + - - -
31B VAL* 3.4 5.2 - - - +
32B THR* 2.9 47.3 + - - +
71B ILE* 3.7 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.5 0.4 - - + -
9B SER* 1.3 82.7 - - - +
11B GLU* 1.3 63.8 + - - +
12B PHE* 4.0 22.2 - - + -
29B VAL* 4.3 2.5 - - + -
30B LYS 3.3 8.1 - - - +
31B VAL* 4.2 17.3 - - + -
67B LYS* 2.9 50.1 + - + +
70B VAL* 3.6 31.0 - - + -
71B ILE* 3.8 12.0 - - + +
105B ILE* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 5.3 6.0 + - - +
10B VAL* 1.3 76.2 - - - +
12B PHE* 1.3 67.2 + - - +
13B ILE* 3.9 21.9 + - + +
28B ILE 3.5 1.4 - - - +
29B VAL* 3.3 4.0 - - - +
30B LYS* 2.7 64.4 + - + +
32B THR* 5.5 1.2 + - - -
67B LYS* 4.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.0 9.9 - - + -
11B GLU* 1.3 81.6 - - - +
13B ILE* 1.3 62.3 + - - +
14B PRO* 3.4 10.4 - - - +
27B VAL* 3.7 22.0 - - + -
28B ILE 3.4 4.5 - - - -
29B VAL* 3.9 17.7 - - + -
43B ALA* 4.4 5.8 - - + -
50B MET* 3.7 23.8 - - + -
51B LYS* 3.9 22.2 + - + +
54B SER* 3.6 31.2 + - - +
55B GLU* 5.0 1.7 + - - +
66B ILE* 4.9 2.0 - - + -
67B LYS* 4.8 3.1 - - - +
101B ALA* 3.7 45.5 - - + -
105B ILE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 4.0 24.2 - - + +
12B PHE* 1.3 75.5 - - - +
14B PRO* 1.3 66.5 - - + +
15B VAL* 3.5 6.7 + - + +
27B VAL* 4.0 2.1 - - - +
28B ILE* 2.6 48.9 + - + +
30B LYS* 4.2 24.5 - - + +
378B VAL* 5.0 5.8 - - + -
382B THR* 3.8 30.1 - - + -
386B PHE* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE 3.4 10.8 - - - +
13B ILE* 1.3 86.0 - - + +
15B VAL* 1.3 62.5 + - - +
16B ASN* 4.0 3.5 + - + +
26B THR 3.8 5.4 - - - +
27B VAL* 4.5 3.3 - - + -
47B PRO* 3.8 21.3 - - + +
48B GLU* 3.5 27.4 - - - +
51B LYS* 3.6 31.4 - - + +
382B THR* 3.7 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.7 11.0 - - + +
14B PRO* 1.3 78.4 - - - +
16B ASN* 1.3 60.6 + - - +
17B VAL* 4.8 2.5 - - + -
24B GLU 4.1 0.2 - - - +
25B ASN* 3.1 27.4 - - - +
26B THR* 2.9 23.8 + - + +
28B ILE* 3.7 28.7 - - + -
47B PRO* 4.5 0.4 - - - +
345B LEU* 4.2 24.9 - - + -
349B LEU* 5.2 5.4 - - + -
377B PHE* 5.0 2.9 - - + -
378B VAL* 5.3 1.8 - - + -
381B VAL* 3.9 23.3 - - + -
382B THR* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 4.0 2.2 + - + +
15B VAL* 1.3 72.5 - - - +
17B VAL* 1.3 68.7 + - - +
24B GLU 4.2 2.1 - - - +
25B ASN* 4.0 16.1 + - - +
47B PRO* 3.9 31.5 - - - +
48B GLU* 5.1 12.3 + - - +
381B VAL* 4.6 15.8 + - - +
----------------------------------------------------------
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