Contacts of the strand formed by residues 118 - 127 (chain B) in PDB entry 4ZHF
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 HIS 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.6 5.1 - - - -
112B SER* 5.1 6.4 + - - -
113B THR* 2.7 29.3 + - - -
114B ASN* 3.1 46.5 + - - +
117B GLN* 1.3 87.4 - - + +
119B ALA* 1.3 60.4 + - - +
137B LEU* 5.1 4.2 - - + +
138B TYR 3.2 9.6 - - - +
144B LEU* 4.3 16.6 - - + -
148B LEU* 4.0 35.1 - - + +
203B SO4 3.6 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.8 20.0 - - + -
31B TRP* 4.0 3.1 - - + -
110B VAL* 5.5 0.4 - - + -
112B SER 3.2 7.4 - - - +
113B THR* 3.4 17.0 - - - +
118B HIS* 1.3 80.2 - - - +
120B MET* 1.3 63.9 + - - +
121B VAL* 4.7 0.2 - - + -
137B LEU* 3.5 8.0 - - - +
138B TYR* 2.7 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.9 1.0 - - - +
111B VAL* 2.9 40.4 + - + -
112B SER* 2.8 30.0 + - - +
119B ALA* 1.3 76.8 - - - +
121B VAL* 1.3 67.0 + - - +
135B ILE* 4.6 4.7 - - + -
136B THR 3.2 7.6 - - - +
137B LEU* 3.8 15.0 - - + -
151B ASN* 4.2 20.0 - - - +
152B PHE* 3.7 34.8 - - + -
155B PHE* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 4.2 14.4 - - + -
56B TYR* 4.9 2.9 - - - +
108B VAL* 3.7 18.8 - - + -
109B ARG 3.6 13.0 - - - +
110B VAL* 4.3 9.6 - - + +
111B VAL* 4.5 0.4 - - - -
119B ALA* 4.7 0.2 - - + -
120B MET* 1.3 81.9 - - - +
122B PHE* 1.3 62.3 + - - +
123B PHE* 3.4 32.8 - - + -
135B ILE* 3.3 6.8 - - - -
136B THR* 2.9 35.6 + - - +
138B TYR* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 24.0 - - + -
13B LEU* 4.0 22.4 - - + -
16B VAL* 3.6 36.1 - - + -
107B LEU* 5.1 4.7 - - + -
108B VAL* 3.5 3.6 - - - -
109B ARG* 2.8 52.8 + - + +
111B VAL* 3.9 5.5 - - + +
121B VAL* 1.3 73.2 - - - +
123B PHE* 1.3 63.0 + - - +
124B LYS* 3.7 31.4 - - + -
133B PHE* 3.9 31.2 - + + -
134B LYS 3.6 7.9 - - - -
135B ILE* 4.2 6.7 - - + +
155B PHE* 5.6 0.2 - + - -
159B LEU* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 4.3 2.7 - - - -
83B PHE* 4.1 12.3 - + - -
106B TYR* 3.7 18.2 - + + +
107B LEU 3.3 5.6 - - - +
108B VAL* 3.8 28.9 - - + -
121B VAL* 3.4 35.2 - - + -
122B PHE* 1.3 79.1 - - - +
124B LYS* 1.3 61.2 + - - +
133B PHE* 3.2 7.8 - - - +
134B LYS* 2.9 61.3 + - + +
136B THR* 3.6 19.1 - - - -
138B TYR* 3.8 6.1 - - - -
202B 4OL 3.9 11.4 - - + -
204B SO4 3.6 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP 5.4 1.8 + - - -
178A GLY* 5.1 5.1 + - - -
10B ALA* 4.1 13.9 - - + -
11B PRO 5.3 2.2 - - - +
13B LEU* 4.4 22.9 - - + -
105B SER* 4.5 6.2 + - - -
106B TYR* 3.4 2.8 - - - -
107B LEU* 2.7 52.7 + - + +
122B PHE* 3.7 21.1 - - + -
123B PHE* 1.3 76.9 - - - +
125B LYS* 1.3 65.1 + - - +
126B VAL* 4.7 9.1 - - - +
131B GLU* 3.1 33.6 + - + +
132B TYR 3.3 10.5 - - - +
133B PHE* 4.6 1.8 - - + -
202B 4OL 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.0 11.1 - - + +
105B SER* 3.2 7.4 - - - +
106B TYR* 3.5 34.1 - - + -
124B LYS* 1.3 76.5 - - - +
126B VAL* 1.3 65.6 + - - +
127B SER* 3.8 22.3 + - - -
130B ARG 3.6 0.3 - - - +
131B GLU* 3.5 3.1 - - - +
132B TYR* 2.8 42.6 + - + +
202B 4OL 3.1 74.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLY* 4.1 24.9 - - - +
103B LEU* 3.5 5.1 - - - +
104B THR* 2.9 42.8 + - - +
105B SER* 2.9 27.1 + - - +
124B LYS* 4.7 4.7 - - - +
125B LYS* 1.3 78.0 - - - +
127B SER* 1.3 63.3 + - - +
129B ASN* 3.9 24.2 - - - +
130B ARG 3.3 9.0 - - - +
131B GLU* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO 4.9 2.3 + - - -
102B GLY* 3.4 13.0 + - - -
103B LEU* 4.4 5.7 + - - +
125B LYS* 3.8 27.9 + - - -
126B VAL* 1.3 75.4 - - - +
128B GLN* 1.3 95.0 + - - +
129B ASN 3.0 0.2 - - - -
130B ARG* 2.9 25.1 + - - +
132B TYR* 4.1 11.6 - - - -
----------------------------------------------------------
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