Contacts of the strand formed by residues 105 - 115 (chain B) in PDB entry 1QQW
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 LYS 105 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.3 5.2 - - - +
86B GLU* 3.5 0.2 - - - -
87B VAL* 3.2 30.1 + - + +
98B LYS* 3.3 17.5 + - - +
99B VAL* 4.0 11.0 - - - +
101B GLU* 3.3 37.6 + - + +
102B HIS* 3.0 41.8 + - + +
103B ILE 3.1 3.2 + - - -
104B GLY* 1.3 74.9 - - - +
106B LYS* 1.3 65.8 + - - +
107B THR* 4.1 13.2 + - - +
139B GLU* 3.2 34.0 + - - -
380B ARG* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 3.7 38.8 - - + -
85B PHE 3.2 3.8 - - - +
86B GLU* 3.4 24.7 + - + +
104B GLY* 3.3 13.1 + - - +
105B LYS* 1.3 79.2 - - - +
107B THR* 1.3 65.0 + - - +
108B PRO* 4.2 4.5 - - - +
380B ARG* 5.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 4.1 2.9 - - - -
85B PHE* 2.8 43.3 + - - +
99B VAL* 3.9 22.4 + - + +
105B LYS* 4.1 15.6 + - - +
106B LYS* 1.3 77.5 + - - +
108B PRO* 1.3 70.0 - - - +
109B ILE* 3.3 2.8 - - - +
136B PHE* 5.0 2.7 - - + -
137B TYR 3.5 31.4 - - - +
138B THR* 4.0 17.3 - - + +
139B GLU* 4.7 4.5 - - - +
380B ARG* 3.7 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY 3.7 11.0 - - - +
84B TYR* 4.1 2.7 - - + -
106B LYS 4.2 4.0 - - - +
107B THR* 1.3 86.2 - - - +
109B ILE* 1.3 61.4 + - - +
136B PHE* 3.9 0.2 - - - -
137B TYR* 3.1 35.2 + - + -
379B TYR* 3.4 27.1 - - - +
380B ARG* 3.3 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 3.8 8.5 - - - +
83B GLY 3.3 22.5 + - - +
84B TYR* 3.2 33.4 - - - +
85B PHE* 3.8 3.8 - - + -
107B THR 3.3 12.1 - - - +
108B PRO* 1.3 77.6 - - - +
110B ALA* 1.3 59.6 + - - +
111B VAL* 3.8 24.7 - - + -
134B VAL* 4.2 9.0 - - + -
135B LYS 3.0 9.9 - - - +
136B PHE* 3.4 37.0 - - + -
137B TYR* 4.1 5.9 - - - -
316B LEU* 4.4 12.1 - - + -
317B VAL 4.1 1.6 - - - +
318B LEU* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 3.9 1.1 - - - -
82B PHE* 3.7 29.2 - - + -
109B ILE* 1.3 74.5 - - - +
111B VAL* 1.3 64.4 + - - +
133B ALA 3.6 0.2 - - - +
134B VAL* 3.2 6.6 - - - -
135B LYS* 2.8 37.7 + - + -
137B TYR* 3.9 15.5 - - - +
332B ILE* 3.9 17.5 - - + -
334B PHE* 3.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 3.2 4.0 - - - -
81B ALA 3.0 36.2 + - - +
109B ILE* 3.8 13.9 - - + -
110B ALA* 1.3 82.4 - - - +
112B ARG* 1.3 65.3 + - - +
113B PHE* 3.5 22.5 - - + -
132B PHE* 3.4 28.3 - - + -
133B ALA 3.2 13.9 - - - +
134B VAL* 4.0 10.1 - - + -
316B LEU* 5.7 2.2 - - + -
318B LEU* 3.7 26.7 - - + -
332B ILE* 5.7 0.6 - - - +
334B PHE* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 2.7 46.8 - - - +
75B HIS* 2.5 31.7 + - - +
76B ALA 3.4 15.0 + - - -
78B GLY* 3.9 14.3 - - - +
79B ALA 3.1 22.4 - - - +
80B GLY* 4.3 1.1 - - - -
111B VAL* 1.3 79.9 - - - +
113B PHE* 1.3 63.9 + - - +
114B SER* 3.5 21.0 + - - -
131B GLY 3.4 4.3 - - - +
133B ALA* 3.2 26.7 + - + +
325B TYR* 4.1 10.9 + - - -
329B VAL* 3.9 11.3 - - + +
330B GLU* 4.4 1.2 + - - -
332B ILE* 3.8 11.2 - - + -
334B PHE* 4.0 17.7 - - + -
600B HEM 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 2.9 1.8 - - - -
79B ALA 2.8 30.0 + - - +
81B ALA* 5.4 0.2 - - + -
111B VAL* 3.5 18.2 - - + -
112B ARG* 1.3 76.3 - - - +
114B SER* 1.3 68.5 + - - +
131B GLY 2.8 12.6 - - - +
132B PHE* 3.4 43.1 - + - -
209B HIS* 3.1 42.2 - + + +
212B MET* 3.3 21.1 - - + -
265B LEU* 3.8 28.7 - - + -
277B TRP* 4.1 9.9 - + - -
318B LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.3 24.5 + - - +
77B LYS 2.9 17.9 - - - -
78B GLY* 3.7 2.0 - - - -
112B ARG* 3.5 20.3 + - - -
113B PHE* 1.3 81.6 - - - +
115B THR* 1.3 64.9 + - - +
130B ARG* 3.3 14.8 - - - +
131B GLY* 2.8 29.2 + - - -
209B HIS* 4.2 7.6 - - - -
600B HEM 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.0 31.3 + - - -
77B LYS* 3.0 27.3 + - - +
114B SER* 1.3 78.1 - - - +
116B VAL* 1.3 67.7 + - - +
118B GLY* 4.6 7.7 + - - -
122B SER* 4.5 3.8 + - - -
123B ALA 4.4 9.9 - - - +
124B ASP* 3.8 27.6 - - - +
126B VAL* 5.1 3.1 - - + +
128B ASP* 4.0 10.1 - - + +
129B PRO 3.8 5.8 - - - -
130B ARG* 4.2 17.3 - - - +
----------------------------------------------------------
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