Contacts of the strand formed by residues 91 - 99 (chain A) in PDB entry 1X5K
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 PRO 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR 3.7 9.9 - - - +
89A ASP 4.5 2.2 - - - +
90A THR* 1.3 90.2 - - + +
92A TYR* 1.3 61.3 + - - +
93A TYR* 3.7 27.7 - - + +
112A GLN* 4.3 23.8 - - + +
113A PHE 4.6 4.5 - - - +
114A ARG* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 4.6 16.8 - + - -
59A SER 4.6 4.7 - - - -
60A THR* 3.2 40.6 - - + +
86A LEU* 4.5 17.3 - - + +
87A THR* 3.0 36.4 + - - -
90A THR* 3.2 50.6 + - + +
91A PRO* 1.3 73.0 - - - +
93A TYR* 1.3 61.8 + - - +
94A PHE* 3.5 34.7 - + + -
111A VAL 3.5 1.7 - - - +
112A GLN* 4.9 0.2 - - - -
113A PHE 3.2 30.7 + - - +
115A THR* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.4 13.3 - - - +
59A SER 3.6 9.0 + - - +
60A THR 3.6 17.7 - - - -
61A ASP* 3.7 10.8 - - - -
62A VAL* 3.4 45.5 - - + +
69A TRP* 3.4 31.8 - - + -
91A PRO* 3.7 23.1 - - + +
92A TYR* 1.3 72.2 - - - +
94A PHE* 1.3 61.7 + - - +
110A ALA* 4.4 14.1 - - + -
111A VAL 3.4 5.2 - - - +
112A GLN* 3.5 44.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.3 17.0 - - + -
37A ILE* 3.2 35.4 - - + -
39A VAL* 4.7 8.3 - - + -
56A ILE* 4.8 8.1 - - + -
57A TYR 3.3 4.9 - - - +
58A TYR* 3.5 27.6 - + + -
83A ILE* 4.2 15.7 - - + -
86A LEU* 4.6 9.2 - - + -
92A TYR* 3.5 43.3 - + + -
93A TYR* 1.3 72.7 - - - +
95A LYS* 1.3 66.2 + - - +
96A ILE* 5.6 1.3 - - + -
111A VAL* 3.0 42.2 + - + +
113A PHE* 4.1 21.1 - + + -
115A THR* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE 4.0 0.2 - - - +
56A ILE* 3.0 10.6 - - - +
57A TYR* 2.8 48.3 + - + +
66A ILE* 3.8 22.3 - - - +
69A TRP* 3.2 46.0 - - + +
94A PHE* 1.3 81.9 - - - +
96A ILE* 1.3 63.5 + - - +
107A MET* 4.1 16.8 - - + +
108A SER* 3.7 26.9 - - - +
109A GLU 4.5 0.4 - - - +
110A ALA* 4.2 15.7 - - + +
111A VAL* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.3 20.9 - - + +
25A VAL* 3.6 31.4 - - + -
27A VAL* 5.6 0.4 - - + -
39A VAL* 3.5 33.0 - - + -
40A ASN 3.9 1.6 - - - +
41A TRP* 3.5 53.2 - - + -
54A TYR* 5.3 0.2 - - + -
55A ILE 3.8 1.8 - - - -
56A ILE* 4.2 11.9 - - + -
94A PHE* 5.6 1.3 - - + -
95A LYS* 1.3 81.7 - - - +
97A GLN* 1.3 70.1 + - - +
107A MET* 5.1 1.1 - - - -
108A SER* 3.2 25.9 + - - +
111A VAL* 5.7 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 4.4 7.9 - - - -
54A TYR* 3.2 27.9 - - - +
55A ILE* 3.0 43.0 + - + +
57A TYR* 2.4 32.0 + - + -
96A ILE* 1.3 77.5 - - - +
98A ALA* 1.3 63.4 + - - +
99A ARG 4.8 0.2 - - - +
104A MET* 3.0 31.2 - - - +
105A GLY 3.0 20.0 + - - +
106A PRO 4.4 7.6 - - - +
107A MET* 4.2 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 3.0 34.2 - - + +
20A SER 5.1 4.0 - - - +
22A PRO* 5.1 5.9 - - + +
44A PRO* 4.4 20.2 - - + -
51A ILE* 4.6 7.4 - - + -
54A TYR* 3.8 22.4 - - + -
97A GLN* 1.3 78.5 - - - +
99A ARG* 1.3 58.8 + - - +
105A GLY* 3.3 14.1 + - - +
106A PRO 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 4.9 0.9 - - - -
51A ILE* 4.0 4.1 - - - +
52A THR* 3.5 22.3 + - - -
53A GLY* 2.9 41.6 + - - +
54A TYR* 4.6 0.6 - - - +
55A ILE* 4.1 20.0 - - + -
97A GLN* 4.3 0.8 + - - -
98A ALA* 1.3 74.6 - - - +
100A ASN* 1.3 72.9 + - - +
101A SER* 4.7 7.9 + - - +
102A LYS 5.3 2.6 + - - -
103A GLY* 2.9 19.8 - - - +
104A MET* 3.6 28.9 - - + +
----------------------------------------------------------
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