Contacts of the strand formed by residues 81 - 90 (chain P) in PDB entry 3QUM
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 GLN 81 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.7 9.9 - - - -
50A ARG* 6.2 1.6 - - - +
65P ILE 4.0 0.2 - - - +
66P LEU* 3.9 2.6 - - - -
67P LEU* 3.0 44.2 + - + +
79P THR 4.1 7.4 + - - +
80P GLY* 1.3 77.5 - - - +
82P VAL* 1.3 61.9 + - - +
83P PHE* 3.7 22.4 - - + -
112P ALA* 4.1 2.9 - - - +
113P GLU* 3.4 34.9 + - - +
115P THR* 4.4 7.9 + - - +
118P VAL* 3.5 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.3 10.9 - - + -
32A PHE* 4.4 20.4 - - + -
50A ARG* 4.7 17.3 - - - +
97B ARG* 3.8 39.6 - - + +
98B LEU* 4.6 7.4 - - + -
64P VAL* 4.9 7.6 - - + -
65P ILE 3.7 12.1 - - - +
66P LEU* 3.9 20.4 - - + -
81P GLN* 1.3 71.7 - - - +
83P PHE* 1.3 89.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 4.4 3.1 - - - -
97B ARG* 4.1 12.1 - - - -
64P VAL* 4.2 3.1 - - - -
65P ILE* 2.9 36.4 + - + +
67P LEU* 3.7 19.3 - - + -
81P GLN* 3.7 16.8 - - + -
82P VAL* 1.3 95.1 - - - +
84P GLN* 1.3 67.6 + - - +
108P LEU* 4.5 16.3 - - + +
109P SER* 3.9 12.3 - - - -
110P GLU* 3.5 38.6 - - + -
111P PRO 3.8 2.9 - - - -
112P ALA* 3.1 41.5 - - + -
113P GLU 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER 5.2 0.3 - - - +
32B TYR* 4.8 1.2 - - - -
33B TRP* 2.9 41.6 + - + +
35B HIS* 5.6 0.2 + - - -
95B SER* 2.8 38.8 + - - +
96B GLY* 3.6 16.8 + - - +
97B ARG* 3.5 1.8 - - - +
98B LEU* 2.6 50.2 - - + +
64P VAL* 3.5 12.8 - - + +
83P PHE* 1.3 74.4 - - - +
85P VAL* 1.3 62.2 + - - +
108P LEU* 3.9 2.2 - - - -
109P SER* 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.1 27.4 - - + -
63P SER* 3.0 41.2 + - - +
64P VAL* 3.7 0.4 - - - -
65P ILE* 3.7 25.4 - - + -
84P GLN* 1.3 72.0 - - - +
86P SER* 1.3 64.6 + - - +
87P HIS 4.3 11.2 - - - +
88P SER* 4.9 4.5 - - - -
106P LEU* 3.9 30.5 - - + -
107P ARG 4.1 11.7 - - - +
108P LEU* 4.7 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER 3.4 15.8 + - - -
31B SER* 3.7 26.9 + - - -
33B TRP* 4.3 3.8 - - - -
52B ASN* 3.0 24.8 - - - +
53B SER* 3.9 1.7 - - - -
54B THR* 4.3 4.0 + - - -
84P GLN 3.6 4.0 + - - -
85P VAL* 1.3 74.9 - - - +
87P HIS* 1.3 63.6 + - - +
107P ARG* 3.0 43.7 + - - -
109P SER* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 3.3 31.6 + - - +
54B THR* 3.3 24.1 + - - -
85P VAL* 3.7 3.3 - - - -
86P SER* 1.3 81.5 - - - +
88P SER* 1.3 74.2 + - - +
89P PHE* 2.9 42.3 - + + -
107P ARG* 2.9 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B THR* 5.1 1.0 + - - -
59P ILE* 3.8 19.3 - - - +
60P ARG 5.4 6.3 - - - -
85P VAL* 4.9 4.7 - - - -
87P HIS* 1.3 91.4 + - - +
89P PHE* 1.3 66.6 + - - +
90P PRO* 3.7 4.9 - - - +
104P MET* 3.5 15.7 - - - -
105P LEU 3.6 3.4 - - - -
106P LEU* 4.0 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P TRP* 4.0 19.1 - + - -
87P HIS* 2.9 55.9 - + + -
88P SER* 1.3 76.2 + - - +
90P PRO* 1.4 68.8 - - - +
104P MET* 3.4 4.8 - - - +
105P LEU* 2.7 45.6 + - + +
107P ARG* 4.2 5.4 - - - -
237P TRP* 3.8 7.4 - - + -
241P THR* 4.4 14.8 - - - +
245P ASN* 3.5 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 90 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P ALA* 4.3 5.4 - - + -
59P ILE* 3.4 26.7 - - + -
88P SER* 3.7 12.8 - - - +
89P PHE* 1.4 94.5 - - - +
91P HIS* 1.3 64.3 + - - +
92P PRO* 3.6 7.1 - - - +
95P MET* 3.8 26.7 - - - +
103P LEU 3.7 5.6 - - - +
104P MET* 4.0 8.5 - - + -
237P TRP* 3.8 4.1 - - - -
----------------------------------------------------------
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