Contacts of the strand formed by residues 109 - 117 (chain A) in PDB entry 5T5I
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 TYR 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY* 3.5 20.9 - - - +
54A VAL 3.7 14.6 - - - -
55A ASP* 3.8 31.4 - - + -
104A TYR* 3.0 41.8 + + + +
105A ALA* 3.6 13.2 + - - +
107A MET* 3.8 31.4 - - + -
108A GLY* 1.4 77.3 - - - +
110A THR* 1.3 62.6 + - - +
111A THR 4.2 2.9 - - - +
134A ILE* 5.2 0.3 - - - +
135A ILE* 3.9 7.2 - - - +
382A LEU 4.9 4.4 + - - -
395A TYR* 3.7 25.0 - + + +
399A ILE* 6.1 3.1 - - + -
442A THR* 3.4 35.4 + - + +
443A ARG* 4.5 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 3.2 27.9 + - - -
53A GLY 3.0 3.6 + - - -
54A VAL* 5.5 0.7 - - - +
109A TYR* 1.3 76.6 - - - +
111A THR* 1.4 62.3 + - - +
134A ILE* 5.2 3.1 - - + -
135A ILE* 3.4 10.9 - - - -
136A ASP 2.9 22.3 + - - -
466A ASP* 3.5 17.1 + - + +
496A VAL* 3.9 17.7 - - + -
497A LEU 3.9 17.9 - - - +
498A LYS* 3.4 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY 3.2 6.7 + - - +
54A VAL* 3.4 27.5 - - + +
55A ASP* 2.9 23.4 + - - +
109A TYR* 3.8 3.6 - - - -
110A THR* 1.4 80.8 + - - +
112A ALA* 1.3 64.6 + - - +
113A MET* 3.5 24.5 - - + -
135A ILE* 4.8 1.8 - - - -
136A ASP* 3.3 17.4 - - + +
452A LEU* 4.8 11.4 - - + -
456A LYS* 3.7 26.7 - - + +
466A ASP* 4.3 1.9 + - - -
518A TYR* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 3.4 11.7 - - + -
60A ILE* 4.1 7.4 - - + +
104A TYR* 3.7 41.7 - - + +
111A THR* 1.3 76.3 - - - +
113A MET* 1.3 71.6 + - - +
114A GLU 4.2 0.2 + - - -
135A ILE* 3.9 12.5 - - + +
136A ASP 3.1 6.3 + - - -
137A HIS* 3.3 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP 3.0 17.8 + - - +
56A PRO* 3.9 7.6 - - + +
57A HIS* 4.1 0.2 - - - -
58A SER* 3.1 30.3 + - - +
60A ILE* 4.5 3.1 - - - -
111A THR* 3.5 24.0 - - + -
112A ALA* 1.3 99.0 - - - +
114A GLU* 1.4 59.3 + - - +
115A ALA 3.5 0.3 + - - -
137A HIS* 3.6 4.5 - - - -
138A ALA* 3.4 34.5 - - + +
140A TYR* 3.2 38.6 - - + +
175A TYR* 5.4 3.1 - - - -
450A LEU* 4.1 18.4 - - + -
452A LEU* 4.9 7.6 - - + -
518A TYR* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 3.4 2.9 - - - -
59A HIS* 3.6 8.9 + - - -
60A ILE* 2.8 33.4 + - + -
61A ALA 2.9 30.3 + - - +
64A LYS* 5.8 0.7 - - - +
65A VAL* 4.3 3.7 - - - +
113A MET* 1.4 67.6 - - - +
115A ALA* 1.3 59.6 + - - +
116A ALA 3.0 36.2 + - - +
117A MET* 4.9 0.9 - - + -
125A THR* 4.0 12.3 - - + +
129A PHE* 3.5 27.7 - - + -
138A ALA 2.9 12.6 + - - +
139A ALA* 3.5 6.3 - - + -
140A TYR* 3.0 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 3.4 44.9 - - + +
58A SER 2.9 18.6 + - - +
59A HIS* 3.8 10.5 - - + -
113A MET 3.5 0.8 + - - -
114A GLU* 1.3 73.7 - - - +
116A ALA* 1.3 57.1 + - - +
140A TYR* 3.6 14.9 - - + +
178A KCX 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 3.8 20.4 - - + +
64A LYS* 2.9 32.0 + - - +
114A GLU* 3.0 18.4 + - - +
115A ALA* 1.3 80.7 - - - +
117A MET* 1.3 57.4 + - - +
118A PRO* 3.8 1.9 - - - +
140A TYR 3.7 3.1 - - - -
142A LEU* 4.0 22.2 - - + -
178A KCX 3.9 6.3 - - - +
319A ALA* 4.6 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 4.8 2.7 - - + -
116A ALA* 1.3 71.0 - - - +
118A PRO* 1.4 77.8 - - + +
119A PRO* 3.3 2.1 - - + -
122A ALA* 3.8 18.6 - - - +
125A THR* 3.5 31.4 - - + +
126A HIS* 4.3 2.7 - - - -
139A ALA* 3.7 31.6 - - + -
140A TYR 2.9 16.3 + - - +
141A PRO* 3.3 20.8 - - + +
142A LEU* 3.3 24.3 + - - +
172A THR* 3.6 39.5 - - + +
173A LYS 4.6 0.2 - - - +
174A GLY* 4.2 4.3 - - - -
----------------------------------------------------------
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