Contacts of the strand formed by residues 114 - 125 (chain T) in PDB entry 5HJD
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 114 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T HIS* 3.3 32.5 - - + +
16T ARG* 3.2 8.8 - - - +
17T ALA* 2.9 44.6 + - + +
105T PHE* 3.7 32.3 - - + +
107T HIS* 3.4 44.0 - - + +
113T PRO* 1.3 72.6 - - - +
115T ASN* 1.3 63.6 + - - +
116T HIS* 4.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ARG* 4.3 26.0 + - - +
113K PRO* 5.7 8.1 - - - +
114K VAL 5.2 0.8 + - - -
115K ASN* 3.1 52.1 + - - +
15T HIS 3.9 1.3 - - - +
16T ARG* 3.2 34.3 + - - +
35T PHE* 6.0 0.3 - - - -
113T PRO* 3.6 6.6 + - + +
114T VAL* 1.3 73.3 - - - +
116T HIS* 1.3 60.6 + - - +
117T LEU 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ARG* 4.0 22.6 + - - -
40K GLU* 4.4 21.7 + - + +
115K ASN* 4.5 0.2 + - - -
14T GLY* 3.2 19.9 - - - -
15T HIS* 3.2 32.4 + - + +
35T PHE* 4.8 0.3 - - - -
102T TYR* 3.4 25.8 - + - -
103T ASP 5.4 0.7 - - - -
105T PHE* 4.1 23.8 - + + -
114T VAL* 4.1 6.7 - - + -
115T ASN* 1.3 75.2 - - - +
117T LEU* 1.3 91.7 + - - +
118T ARG* 4.5 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K GLU* 5.3 0.2 - - - +
37K ARG* 2.9 29.0 + - - +
115K ASN* 3.1 52.7 - - + +
116K HIS 4.5 0.4 - - - -
117K LEU* 3.3 30.6 - - + +
12T GLU* 4.6 15.5 - - + +
13T LEU 3.5 4.3 - - - +
14T GLY* 4.1 4.0 - - - -
35T PHE* 3.8 28.5 - - + -
37T ARG* 4.3 10.8 - - - +
115T ASN 4.1 0.8 + - - -
116T HIS* 1.3 93.2 + - - +
118T ARG* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K GLU* 5.2 2.7 - - - +
40K GLU* 3.5 36.1 + - + -
117K LEU* 4.1 1.3 - - - -
11T LEU 3.8 0.3 - - - +
12T GLU* 3.5 8.2 - - - +
13T LEU* 2.6 48.2 + - + +
100T PHE* 3.7 31.1 - - - +
101T ASP 3.3 27.1 + - - +
102T TYR* 4.1 19.0 - - + +
116T HIS* 4.5 9.0 - - - +
117T LEU* 1.3 78.2 - - - +
119T CYS* 1.3 65.1 + - - +
120T GLU* 2.6 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K GLU* 4.4 7.4 + - - +
117K LEU* 3.6 30.8 - - - +
119K CYS* 2.0 47.3 - - + -
11T LEU 3.9 3.6 - - - -
12T GLU* 5.2 7.4 - - - +
118T ARG* 1.3 75.4 - - - +
120T GLU* 1.3 76.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T LYS* 3.7 1.9 - - - +
11T LEU* 2.8 49.1 + - + +
13T LEU* 4.1 12.6 - - + -
100T PHE* 3.6 41.2 - - + -
118T ARG* 2.6 39.9 + - + +
119T CYS* 1.3 87.7 - - - +
121T LYS* 1.3 64.0 + - - +
122T LEU* 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K LYS* 5.9 7.3 - - - +
8T GLN* 3.4 44.8 + - + +
9T VAL 3.7 9.4 - - - +
10T LYS* 4.3 30.4 - - + +
100T PHE* 6.1 0.2 - - - -
120T GLU* 1.3 76.2 + - - +
122T LEU* 1.3 75.0 + - - +
123T THR* 4.1 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T VAL 3.6 1.0 - - - +
8T GLN* 3.1 6.9 - - - +
9T VAL* 2.8 58.1 + - + +
11T LEU* 3.7 31.0 - - + -
47T PHE* 4.7 1.6 - - + -
89T PHE* 3.7 30.7 - - + -
98T VAL* 4.0 28.5 - - + -
100T PHE* 4.0 13.2 - - + -
120T GLU 5.0 1.3 - - - +
121T LYS* 1.3 80.3 - - - +
123T THR* 1.3 60.4 + - - +
124T PHE* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T ALA* 4.5 13.5 - - + -
7T VAL 3.5 2.9 - - - +
8T GLN* 3.4 30.7 + - + +
121T LYS* 4.1 6.9 + - - +
122T LEU* 1.3 75.3 - - - +
124T PHE* 1.3 66.8 + - - +
125T ASN* 4.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T CYS 3.6 2.1 - - - +
6T ALA* 3.7 0.2 - - - -
7T VAL* 2.8 40.7 + - + +
9T VAL* 3.9 5.6 - - + -
89T PHE* 3.5 49.1 - + - -
91T ASN* 5.1 0.9 - - - -
95T PRO* 4.3 25.6 - - + -
122T LEU* 3.8 24.2 - - + -
123T THR* 1.3 75.8 - - - +
125T ASN* 1.3 63.8 + - - +
126T ASN 3.7 0.2 + - - -
127T PRO* 3.7 19.2 - - + +
131T PHE* 3.6 27.8 - + - -
135T LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 125 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T CYS 3.4 4.9 - - - +
6T ALA* 4.6 8.2 - - - +
93T GLU* 5.3 1.2 - - - +
123T THR* 4.2 25.2 + - - +
124T PHE* 1.3 71.8 - - - +
126T ASN* 1.3 80.4 + - - +
127T PRO* 3.4 1.7 - - - +
----------------------------------------------------------
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