Contacts of the strand formed by residues 103 - 115 (chain U) in PDB entry 1H2I
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 PHE 103 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96U VAL* 4.2 12.8 - - + -
97U ASP 3.1 14.6 - - - -
98U LEU* 3.8 34.5 - - + -
101U GLY 4.9 0.9 - - - -
102U LYS* 1.3 73.2 - - - +
104U TYR* 1.3 64.2 + - - +
105U VAL* 4.1 5.2 - - + -
129U SER 3.4 6.2 - - - +
130U GLU 3.7 0.2 - - - -
131U GLY 3.0 23.2 + - - -
132U LEU 2.8 11.9 + - - -
133U LYS* 3.3 26.2 - - - -
134U SER 3.8 2.0 - - - -
135U LYS* 3.5 55.4 - - + -
138U SER* 3.9 20.5 + - - +
97V ASP* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95U PHE* 3.2 19.4 - - + -
96U VAL* 3.6 0.2 - - - -
97U ASP* 2.6 51.4 + - + +
99U ASN* 3.9 24.7 - - + +
100U ASN* 3.5 24.6 + - - -
102U LYS* 3.5 29.8 + - - +
103U PHE* 1.3 72.7 - - - +
105U VAL* 1.3 60.7 + - - +
129U SER 3.4 2.5 - - - -
130U GLU* 3.6 40.4 - - + +
131U GLY* 3.8 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136T ALA* 4.8 0.2 - - - -
93U VAL* 4.8 0.4 - - + -
95U PHE* 3.4 14.8 - - - +
96U VAL* 4.1 21.1 - - + -
103U PHE* 4.4 2.2 - - + -
104U TYR* 1.3 84.0 - - - +
106U GLY* 1.3 61.7 + - - +
107U VAL* 4.0 6.3 - - + -
127U GLY 3.7 0.6 - - - +
128U VAL* 3.4 10.7 - - - +
129U SER* 2.8 39.1 + - - +
130U GLU* 4.9 1.0 - - - +
138U SER* 3.9 25.1 - - - +
139U LEU* 3.6 28.7 - - + +
142U ALA* 3.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136T ALA* 4.5 1.1 - - - -
94U ASP* 2.8 28.2 + - - +
95U PHE* 3.3 23.5 + - - +
105U VAL* 1.3 74.5 - - - +
107U VAL* 1.3 62.5 + - - +
126U TYR* 3.3 25.6 - - - -
127U GLY 3.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U GLN* 3.6 36.6 - - + +
92U ASN 3.6 12.3 - - - +
93U VAL* 3.8 23.6 - - + -
105U VAL* 4.0 8.1 - - + -
106U GLY* 1.3 79.5 - - - +
108U CYS* 1.3 64.0 + - - +
126U TYR* 3.2 8.1 - - - -
127U GLY 2.6 39.6 + - - -
139U LEU* 4.7 0.4 - - + -
142U ALA* 3.6 28.5 - - + +
143U ARG* 4.0 10.5 - - + +
146U ALA* 3.4 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143T ARG* 3.3 39.0 - - - -
91U GLN* 3.3 5.7 - - - +
92U ASN* 2.8 52.8 + - - -
94U ASP* 4.7 0.4 + - - -
107U VAL* 1.3 75.3 - - - +
109U ALA* 1.3 59.7 + - - +
110U PHE* 3.8 18.6 - - - -
124U VAL* 4.4 5.4 - - + -
125U GLY 3.3 7.0 - - - +
126U TYR* 3.6 21.0 - - + -
146U ALA* 4.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88U ILE* 5.0 1.6 - - + -
90U GLN 3.4 7.2 - - - +
91U GLN* 4.0 10.5 - - + +
108U CYS* 1.3 75.1 - - - +
110U PHE* 1.3 63.5 + - - +
111U VAL* 3.9 7.8 + - + +
123U ASP 3.7 0.3 - - - +
124U VAL* 3.2 4.4 - - - -
125U GLY 2.8 35.4 + - - -
146U ALA* 3.6 32.3 - - + +
147U VAL* 3.8 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T ILE* 3.8 31.9 - - + -
91T GLN* 3.3 44.4 - - + -
143T ARG* 4.5 4.3 - - - -
88U ILE* 3.4 6.8 - - - +
89U THR* 2.8 45.5 + - - +
90U GLN* 2.8 41.8 + - + +
108U CYS* 3.8 23.8 - - - -
109U ALA* 1.3 72.3 - - - +
111U VAL* 1.3 60.5 + - - +
122U GLU* 3.8 4.7 - - - +
123U ASP 3.4 2.7 - - - +
124U VAL* 3.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U HIS* 4.0 25.4 - - + -
87U SER 3.4 10.5 - - - +
88U ILE* 4.6 9.0 - - + -
109U ALA* 4.5 5.4 - - + -
110U PHE* 1.3 79.3 - - - +
112U ARG* 1.3 63.8 + - - +
113U VAL 4.8 0.4 - - - +
122U GLU* 3.2 5.4 - - - +
123U ASP 3.0 29.9 + - - -
147U VAL* 3.7 31.4 - - + +
150U GLY* 3.8 16.6 - - - +
151U LEU* 3.8 22.2 - - + +
154U ALA* 3.8 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87T SER* 5.0 5.5 - - - -
86U HIS* 3.0 4.3 - - - -
87U SER* 2.9 43.8 + - - +
89U THR* 4.0 22.8 - - + +
110U PHE 4.2 0.8 + - - -
111U VAL* 1.3 72.6 - - - +
113U VAL* 1.3 65.4 + - - +
114U GLN* 2.9 34.8 + - - +
118U GLY 4.8 0.6 + - - -
120U TYR* 3.6 46.4 - - + +
121U HIS 3.6 5.2 - - - +
122U GLU* 3.8 25.8 - - + -
120V TYR* 4.9 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84U TRP* 4.1 13.2 - - + -
85U ALA 3.0 13.0 - - - +
86U HIS* 3.9 7.9 - - + +
111U VAL* 4.0 0.6 - - + -
112U ARG* 1.3 75.4 - - - +
114U GLN* 1.3 65.5 + - - +
120U TYR* 3.3 5.9 - - - +
121U HIS 2.9 41.6 + - - +
151U LEU* 4.8 3.4 - - + -
154U ALA* 3.5 31.6 - - + +
155U LEU* 3.6 24.2 - - + -
158U PHE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U PHE* 3.5 16.1 - - + -
27U GLY* 3.6 20.2 - - - -
84U TRP* 3.1 4.5 - - - +
85U ALA 2.7 39.5 + - - +
112U ARG* 2.9 28.2 + - - +
113U VAL* 1.3 76.7 - - - +
115U LEU* 1.3 73.0 + - - +
118U GLY* 3.5 25.1 - - - +
119U SER 3.3 14.8 - - - +
120U TYR* 4.3 0.4 - - + +
120V TYR* 3.2 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T TYR* 4.1 13.7 - - + +
26U PHE* 3.4 6.1 - - - -
31U TYR* 3.6 18.8 - - + +
79U PHE* 4.0 21.3 - - + -
83U GLY 3.3 9.9 - - - +
84U TRP* 3.9 12.8 - - + -
113U VAL* 5.1 0.2 - - + -
114U GLN* 1.3 88.3 + - - +
116U LYS* 1.3 55.7 + - - +
117U ASP* 2.7 18.2 + - + -
118U GLY* 2.8 13.0 + - - -
119U SER* 2.9 29.1 + - - +
158U PHE* 3.2 47.6 - - + -
----------------------------------------------------------
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