Contacts of the strand formed by residues 107 - 121 (chain C) in PDB entry 4QKB
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 107 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 3.5 4.2 - - - -
78C LYS* 2.7 46.0 + - - +
81C TRP* 3.7 21.5 - - + +
89C MSE 4.5 9.0 - - + -
103C LEU* 5.4 5.2 - - + -
104C LEU 5.7 1.1 - - - +
106C SER* 1.3 76.9 - - - +
108C HIS* 1.3 65.0 + - - +
109C VAL* 3.5 1.9 + - + -
200C VAL* 3.4 33.0 - - + -
201C ILE 3.6 12.8 - - - +
202C CYS* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 4.1 12.2 - + + -
70C ILE* 4.7 1.1 - - + -
75C GLU* 3.2 33.3 + - + +
76C THR 3.6 5.2 - - - -
77C GLU* 3.4 25.5 + - - +
106C SER 4.3 0.6 + - - -
107C VAL* 1.3 69.4 - - - +
109C VAL* 1.3 70.6 + - - +
110C LEU* 3.8 22.7 - - + +
200C VAL* 3.5 1.7 - - - -
201C ILE* 2.7 51.5 + - + +
203C ARG* 3.2 31.3 + - - +
302C AKG 3.2 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.8 43.1 - - + -
56C LEU* 4.4 10.8 - - + +
75C GLU* 3.3 5.4 - - - +
76C THR* 2.8 57.0 + - + +
78C LYS* 4.3 7.9 - - + -
81C TRP* 4.5 3.4 - - + -
107C VAL 4.1 8.3 - - - +
108C HIS* 1.3 78.2 - - - +
110C LEU* 1.3 62.2 + - - +
198C ILE* 3.9 13.0 - - + -
199C SER 3.4 9.4 - - - +
200C VAL* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.7 27.6 - - + -
73C PHE* 3.8 17.0 - - + -
74C ARG 4.0 0.7 - - - +
75C GLU* 3.7 20.4 - - + +
108C HIS* 3.8 12.1 - - + +
109C VAL* 1.3 74.6 - - - +
111C ASP* 1.3 62.5 + - - +
112C LEU* 4.1 16.7 - - + +
118C ILE* 3.8 20.0 - - + -
197C ARG* 3.7 1.2 + - - +
198C ILE* 3.3 6.7 - - - +
199C SER* 2.8 46.6 + - - +
201C ILE* 4.1 1.6 - - + -
302C AKG 3.6 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.8 18.3 - - + +
61C TYR* 2.8 22.4 + - - -
73C PHE* 3.2 7.1 - - - +
74C ARG* 2.6 70.6 + - + +
109C VAL 4.3 0.2 - - - -
110C LEU* 1.3 73.3 - - - +
112C LEU* 1.3 64.1 + - - +
196C ARG* 2.9 36.1 + - - +
197C ARG 3.6 3.7 - - - +
198C ILE* 4.6 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.5 31.9 - - + -
71C HIS 4.0 11.0 - - - +
72C GLY 3.6 2.2 - - - +
73C PHE* 3.7 11.9 - - + -
110C LEU* 4.1 11.0 - - + +
111C ASP* 1.3 76.5 - - - +
113C GLU* 1.3 61.0 + - - +
116C GLY 4.8 2.0 - - - -
117C TYR* 4.1 8.1 - - - +
118C ILE* 4.0 23.3 - - + -
179C ILE* 4.5 10.3 - - + -
194C ARG* 3.9 20.9 - - - +
196C ARG* 3.1 5.7 - - - +
197C ARG* 2.7 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 3.8 31.0 - - + +
64C ASP* 5.5 1.4 - - - +
72C GLY* 3.2 32.7 + - - +
112C LEU* 1.3 77.7 - - - +
114C ALA* 1.3 68.0 + - - +
115C ARG* 3.7 21.9 - - - +
116C GLY 3.0 17.4 + - - +
194C ARG* 3.0 14.4 + - - -
196C ARG* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLU* 1.3 75.4 - - - +
115C ARG* 1.3 66.3 + - + +
116C GLY 3.6 1.6 + - - +
182C ASP* 4.5 8.0 + - - +
194C ARG* 3.8 27.7 + - - +
195C GLY* 3.6 29.6 - - - -
196C ARG* 3.7 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLY* 5.6 0.4 - - - -
113C GLU* 3.1 21.8 - - - +
114C ALA* 1.3 80.7 - - + +
116C GLY* 1.3 61.8 + - - +
117C TYR* 3.9 13.2 - - - -
181C ARG* 4.9 4.5 - - - +
182C ASP* 5.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C HIS 3.1 18.6 - - - -
72C GLY* 4.0 9.2 - - - -
112C LEU* 4.8 3.1 - - - -
113C GLU* 3.0 16.3 + - - +
114C ALA 4.1 0.5 - - - +
115C ARG* 1.3 81.7 - - - +
117C TYR* 1.3 57.1 + - - +
181C ARG* 4.3 2.1 - - - -
194C ARG* 2.5 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.8 11.7 + - - -
70C ILE* 3.8 1.7 - - - +
71C HIS* 3.0 67.2 + + + +
112C LEU* 4.1 4.9 - - - +
115C ARG 3.9 9.0 - - - -
116C GLY* 1.3 79.2 - - - +
118C ILE* 1.3 80.8 + - - +
119C LYS* 3.7 26.1 + - + -
179C ILE 3.4 13.5 - - - +
181C ARG* 3.1 67.1 + - + +
194C ARG* 4.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA 3.5 8.7 - - - +
70C ILE* 3.9 19.5 - - + -
110C LEU* 3.8 15.7 - - + -
112C LEU* 4.0 9.4 - - + -
117C TYR* 1.3 87.6 - - - +
119C LYS* 1.3 61.9 + - - +
121C HIS* 3.2 34.1 - - + -
178C GLU* 3.1 25.7 - - - +
179C ILE* 3.0 42.7 + - + +
302C AKG 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.7 19.3 - - - +
105B SER* 6.0 0.4 - - - -
127B PHE* 3.7 35.2 + - + +
205B LEU* 6.0 3.8 - - - -
66C TRP* 2.7 30.7 + - - +
68C ALA 4.0 6.5 - - - +
69C ALA* 2.7 17.8 + - - +
71C HIS* 3.5 12.8 + - - -
117C TYR* 3.7 32.5 + - + -
118C ILE* 1.3 74.1 - - - +
120C PRO* 1.4 72.2 - - + +
121C HIS* 2.8 26.2 + - - +
177C HIS 3.5 1.7 - - - +
178C GLU* 3.8 0.7 - - - -
181C ARG* 4.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 5.4 6.2 - - - +
127B PHE* 4.2 12.6 - - - -
119C LYS* 1.4 89.6 - - + +
121C HIS* 1.3 61.5 + - - +
144C ARG* 5.9 0.2 - - - +
146C VAL* 5.8 2.0 - - + -
176C SER* 3.5 22.0 - - - +
177C HIS 3.4 8.1 - - - +
178C GLU* 3.7 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 6.2 5.6 - - + +
127B PHE* 5.1 5.2 - - + -
69C ALA* 4.1 19.6 - - + +
70C ILE* 5.6 0.4 - - + -
118C ILE* 3.2 23.6 - - + +
119C LYS 2.8 19.1 + - - +
120C PRO* 1.3 75.4 - - - +
122C VAL* 1.3 71.1 + - - +
123C ASP* 3.2 9.6 - - - -
176C SER* 3.3 5.5 - - - -
177C HIS* 2.9 42.4 + + - +
301C MN 2.2 36.8 + - - -
302C AKG 3.0 16.2 + - - -
----------------------------------------------------------
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