Contacts of the strand formed by residues 87 - 98 (chain A) in PDB entry 3KNB
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 GLY 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.9 7.0 - - - -
6A PRO* 3.2 7.8 - - - +
83A GLY* 3.5 0.7 - - - -
84A ASN* 3.0 32.8 + - - +
85A GLU 3.6 0.4 - - - -
86A PHE* 1.3 81.8 - - - +
88A SER* 1.3 63.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.6 2.2 - - - +
6A PRO* 3.7 10.3 - - - +
82A LEU 3.1 15.0 - - - -
83A GLY* 4.4 2.2 - - - -
87A GLY* 1.3 76.1 - - - -
89A ASP* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 3.5 21.1 - - + +
7A LYS* 3.6 13.4 + - - +
8A ILE* 2.8 40.4 + - + +
81A SER* 3.4 2.3 - - - -
82A LEU* 2.9 30.9 + - + +
88A SER* 1.3 78.3 - - - +
90A SER* 1.3 82.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.4 4.4 - - - +
79A THR* 4.2 8.5 - - - -
80A LEU 3.1 12.8 - - - -
81A SER* 4.0 11.9 - - - -
89A ASP* 1.3 89.4 + - - +
91A ALA* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.9 21.8 - - + -
11A LEU* 3.7 25.2 - - + +
79A THR* 3.4 0.9 - - - +
80A LEU* 2.9 30.4 + - - -
90A SER* 1.3 76.6 - - - +
92A THR* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 4.6 - - - +
12A PRO 3.8 8.3 - - - +
13A SER* 4.2 8.1 - - - +
77A LEU* 2.9 48.4 - - + +
78A TYR 2.7 22.2 - - - +
79A THR* 2.9 20.6 + - - +
91A ALA* 1.3 77.3 - - - +
93A VAL* 1.3 59.6 + - - +
94A ASN 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.1 12.8 - - + -
12A PRO* 3.3 24.7 - - + +
13A SER 3.6 5.2 - - - +
15A ILE* 3.8 39.9 - - + -
25A VAL* 5.2 2.9 - - + -
39A TRP* 4.2 17.3 - - + -
77A LEU* 4.0 2.5 - - - -
78A TYR* 2.8 48.8 + - + +
92A THR* 1.3 73.8 - - - +
94A ASN* 1.3 64.5 + - - +
95A ILE* 3.5 10.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 2.8 11.4 + - - +
14A ASP* 3.3 17.6 + - - +
15A ILE 2.9 24.8 + - - -
76A GLY* 3.4 17.7 - - - +
77A LEU* 3.7 21.2 - - + +
93A VAL* 1.3 71.1 - - - +
95A ILE* 1.3 66.8 + - - +
96A HIS* 3.3 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 30.7 - - + +
17A ILE* 4.7 0.2 - - + -
23A LEU* 3.6 27.1 - - + -
25A VAL* 5.0 1.6 - - + -
65A LEU* 4.6 7.9 - - + -
67A ILE* 4.3 10.8 - - + -
74A ASP 4.8 1.6 - - - +
75A GLY* 3.3 5.9 - - - -
76A GLY 2.9 37.4 + - - +
78A TYR* 3.5 43.7 - - + -
93A VAL* 4.1 9.2 - - + +
94A ASN* 1.3 74.8 + - - +
96A HIS* 1.3 63.3 + - - +
97A ILE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 2.8 31.3 + - + +
15A ILE 2.8 20.4 + - - -
16A SER* 3.2 18.8 - - - +
17A ILE* 3.1 27.4 + - - +
75A GLY* 5.2 0.2 - - - -
94A ASN* 3.3 35.3 + - - -
95A ILE* 1.3 73.2 + - - +
97A ILE* 1.3 64.7 + - - +
98A ARG* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.5 13.2 - - + +
19A GLU* 4.0 32.3 - - + +
70A VAL* 3.3 25.6 - - + -
71A GLN 3.6 10.5 - - - +
72A LYS* 3.6 20.9 - - + +
74A ASP* 4.3 1.1 - - + -
75A GLY* 3.5 34.5 - - - +
95A ILE* 4.0 10.1 + - + -
96A HIS* 1.3 79.0 - - - +
98A ARG* 1.3 66.0 + - - +
99A SER* 3.4 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 3.3 30.7 - - - +
17A ILE 2.9 13.2 + - - +
18A ASP* 2.8 55.3 + - - +
19A GLU* 3.6 29.0 + - - +
96A HIS* 5.5 0.9 - - + -
97A ILE* 1.3 72.7 - - - +
99A SER* 1.3 68.0 + - - +
87B ARG* 2.8 33.3 - - - +
94B GLU* 3.2 24.7 + - - -
----------------------------------------------------------
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