Contacts of the strand formed by residues 79 - 91 (chain B) in PDB entry 1QFW
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 VAL 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 2.7 22.3 + - - -
66B SER* 3.9 25.4 - - - +
67B ILE 4.7 1.6 - - - +
68B ARG* 3.9 34.5 - - + +
77B ASN* 3.0 15.7 + - - +
78B PRO* 1.3 72.4 - - + +
80B VAL* 1.3 57.2 + - - +
304I GLN* 6.0 0.2 - - - +
306I TYR* 4.9 4.7 - - + -
230M ASP* 4.2 11.3 - - - +
232M PHE* 3.8 20.9 - - + -
292M TYR* 3.4 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.1 36.8 - - + -
19B GLU 4.6 13.9 - - - +
20B LYS* 4.2 10.3 - - + +
66B SER* 3.1 5.6 - - - -
67B ILE* 2.9 54.5 + - + +
69B LEU* 4.1 13.2 - - + -
78B PRO 2.8 8.6 + - - +
79B VAL* 1.3 75.0 - - - +
81B SER* 1.3 67.9 + - - +
82B TYR* 5.0 0.4 - - + -
292M TYR* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 5.4 1.5 - - - +
64B PHE* 4.7 4.0 - - - -
65B GLU 3.0 12.8 - - - -
80B VAL* 1.3 84.2 - - - +
82B TYR* 1.3 62.0 + - - +
228M THR* 2.7 43.2 + - - +
230M ASP* 3.7 28.4 - - - +
292M TYR* 3.7 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.6 15.3 - - + -
18B VAL* 5.1 5.6 - - + -
29B VAL* 4.2 17.4 - - + +
30B ASN* 3.9 22.9 + - - -
31B THR* 3.8 22.0 - - - +
64B PHE* 3.1 8.7 - - - +
65B GLU* 2.9 65.8 + - + +
66B SER 3.4 7.0 + - - -
67B ILE* 3.1 56.8 - - + +
80B VAL* 4.1 3.1 - - + -
81B SER* 1.3 76.3 - - - +
83B ALA* 1.3 60.8 + - - +
84B VAL* 3.9 5.3 + - + -
228M THR* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 4.7 11.2 - - + +
93A NAG 3.6 26.5 - - + -
16B LEU* 5.4 0.6 - - - +
31B THR* 4.1 9.2 + - - +
32B THR 4.0 4.2 - - - +
59B TYR* 4.0 15.2 + - + +
62B VAL* 4.8 7.0 - - + -
63B ARG 3.6 4.9 - - - +
64B PHE* 3.5 26.7 - - + -
82B TYR* 1.3 74.7 - - - +
84B VAL* 1.3 60.8 + - - +
85B ALA 3.7 1.7 + - - -
228M THR* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN 5.6 0.7 - - - +
31B THR* 4.5 13.2 - - - +
32B THR* 3.7 23.3 - - - +
59B TYR* 4.8 0.2 - - - -
62B VAL* 3.4 7.6 - - - +
63B ARG* 2.6 63.1 + - + +
65B GLU* 4.2 34.3 - - + +
82B TYR* 4.8 3.8 - - + +
83B ALA* 1.3 72.7 - - - +
85B ALA* 1.3 66.7 + - - +
86B LEU* 3.5 4.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 4.9 - - - +
32B THR* 3.0 47.9 + - + +
33B ILE 4.4 0.2 - - - -
34B CYS* 3.9 16.8 - - - -
59B TYR* 3.4 27.4 - - + -
61B ASP 4.0 3.6 - - - -
84B VAL* 1.3 74.4 - - - +
86B LEU* 1.3 65.6 + - - +
87B SER 4.5 0.9 - - - +
88B CYS* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 4.0 12.5 - - - +
61B ASP* 2.8 31.4 + - + +
62B VAL 4.4 1.6 - - - +
63B ARG* 3.6 54.1 - - + +
84B VAL* 3.5 5.1 + - + -
85B ALA* 1.3 75.5 - - - +
87B SER* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 4.9 1.1 - - - -
34B CYS* 3.9 3.1 - - - -
59B TYR* 3.7 4.2 - - - +
60B ARG* 2.8 39.5 + - - -
61B ASP* 3.0 41.9 + - - +
85B ALA* 4.5 1.2 - - - +
86B LEU* 1.3 83.0 + - - +
88B CYS* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B CYS* 4.0 18.6 - - - +
10B ARG 4.3 1.3 - - - +
11B PRO* 3.2 44.2 - - + +
34B CYS* 2.0 59.9 - - + -
58B ASN 3.4 1.6 - - - -
60B ARG* 4.1 6.2 + - - +
85B ALA* 4.3 1.8 - - - -
87B SER* 1.3 75.3 - - - +
89B GLN* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B CYS* 4.1 9.9 - - - -
57B CYS* 3.6 0.5 - - - -
58B ASN* 2.9 35.1 + - - +
59B TYR 4.9 1.8 - - - +
60B ARG* 3.6 38.1 - - + +
88B CYS* 1.3 78.0 - - - +
90B CYS* 1.3 64.1 + - - +
91B ALA* 3.8 4.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 5.1 9.9 - - - +
9B CYS* 4.4 2.4 - - + +
38B CYS* 2.0 51.8 - - - -
39B PRO* 4.6 2.9 - - + -
55B VAL* 4.5 14.7 - - + +
56B VAL* 3.6 5.2 - - - -
57B CYS* 3.5 27.8 - - - -
89B GLN* 1.3 72.6 - - - +
91B ALA* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 3.7 13.4 - - - -
56B VAL 2.7 32.1 + - - +
58B ASN* 5.2 5.1 - - + +
89B GLN* 3.8 6.9 + - + +
90B CYS* 1.3 74.0 - - - +
92B LEU* 1.3 68.2 + - - +
----------------------------------------------------------
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