Contacts of the strand formed by residues 92 - 103 (chain A) in PDB entry 1MWT
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 LYS 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.8 0.9 - - - -
88A VAL* 2.9 47.4 + - + +
89A SER* 3.4 28.6 + - - +
91A ASN* 1.3 90.0 - - + +
93A LYS* 1.3 61.9 + - - +
115A ASN* 6.1 1.1 - - - -
116A PHE 3.4 4.7 - - - +
117A VAL* 4.3 14.4 - - + -
123A TRP* 3.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.4 29.3 + - - +
30A ILE* 3.6 31.9 - - + -
85A ILE* 4.3 7.3 - - + +
86A LYS 3.6 11.7 + - - +
87A LYS* 3.6 26.3 - - + +
88A VAL* 5.4 0.4 - - - -
92A LYS* 1.3 72.3 - - - +
94A ARG* 1.3 60.6 + - - +
95A VAL* 5.2 0.2 - - - -
115A ASN* 3.7 3.2 - - - +
116A PHE* 2.9 36.2 + - + +
123A TRP* 3.4 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS 3.4 2.8 - - - +
85A ILE* 3.6 0.3 - - - -
86A LYS* 2.8 50.4 + - + +
88A VAL* 4.2 21.9 - - + +
92A LYS 4.2 1.0 + - - -
93A LYS* 1.3 74.7 - - - +
95A VAL* 1.3 62.2 + - - +
96A ASP* 2.9 33.2 + - - +
113A GLN* 2.9 49.1 + - + +
114A PHE 3.7 4.5 - - - +
115A ASN* 4.3 6.7 - - - +
176B LYS* 4.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.7 31.6 - - + -
34A ILE* 3.8 20.2 - - + -
83A ARG* 4.5 8.7 - - + -
84A LYS 3.4 13.5 - - - +
85A ILE* 4.0 14.1 - - + -
93A LYS 5.0 0.4 - - - +
94A ARG* 1.3 77.0 - - - +
96A ASP* 1.3 71.7 + - - +
97A ALA* 4.8 2.0 - - + -
113A GLN* 3.2 6.6 - - - +
114A PHE* 2.9 47.9 + - + +
116A PHE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP 3.2 4.9 - - - +
84A LYS* 2.8 48.8 + - + +
86A LYS* 4.6 13.7 + - - +
94A ARG* 2.9 50.8 + - - +
95A VAL* 1.3 71.2 - - - +
97A ALA* 1.3 62.1 + - - +
112A VAL 3.8 8.4 - - - +
113A GLN* 3.8 7.6 - - - +
176B LYS* 5.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.6 24.2 - - + -
81A GLN 3.2 14.8 - - - +
82A ASP 3.9 4.0 - - - -
83A ARG* 3.9 12.6 - - + -
95A VAL* 4.2 3.3 - - + -
96A ASP* 1.3 75.2 - - - +
98A GLN* 1.3 65.6 + - - +
111A ASN* 3.4 6.9 - - - +
112A VAL* 2.9 36.6 + - + +
114A PHE* 4.6 4.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN 3.2 15.8 - - - +
80A ILE* 3.3 3.3 - - - -
81A GLN 3.0 22.4 + - - +
82A ASP* 3.9 20.6 - - + +
97A ALA* 1.3 76.7 - - - +
99A TYR* 1.3 60.3 + - - +
100A LYS* 3.5 19.6 + - - +
109A ASP* 3.1 25.0 + - - +
110A ARG 3.3 18.0 + - - -
111A ASN* 2.8 31.2 + - - +
112A VAL* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.7 13.3 - - + +
70A TYR* 3.0 18.4 + - - -
78A ILE* 3.6 20.4 - - + +
79A ASN 4.0 0.7 - - - -
80A ILE* 3.9 13.2 - - + -
97A ALA 3.9 1.4 + - - -
98A GLN* 1.3 71.6 - - - +
100A LYS* 1.3 61.6 + - - +
101A ILE* 3.6 26.1 + - + -
108A ILE* 3.4 4.9 - - - +
110A ARG 2.8 31.8 + - - +
112A VAL* 3.4 37.9 - - + -
114A PHE* 4.2 12.6 - + - -
130A SER 3.5 16.2 - - - -
131A VAL* 2.8 25.5 + - - -
132A ILE 3.4 5.1 + - - -
134A PRO* 3.5 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP 4.1 0.5 - - - +
78A ILE* 3.4 4.5 - - - +
79A ASN* 2.9 47.6 + - + +
81A GLN* 2.7 40.8 + - - +
82A ASP* 4.9 4.6 + - - -
98A GLN* 4.1 17.7 - - - +
99A TYR* 1.3 74.0 - - - +
101A ILE* 1.3 61.5 + - - +
102A LYS* 5.5 5.7 - - + +
108A ILE 3.0 5.4 - - - +
109A ASP* 3.1 38.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.5 4.9 - - + +
73A LEU* 6.0 0.2 - - + -
75A VAL* 3.8 32.8 - - + -
77A ASP 3.8 2.2 - - - -
78A ILE* 4.2 12.6 - - + -
99A TYR* 3.6 33.2 - - + +
100A LYS* 1.3 78.1 - - - +
102A LYS* 1.3 64.8 + - - +
103A THR* 3.8 8.8 + - + +
106A GLY 4.1 0.5 - - - +
107A ASN* 3.4 3.9 - - - +
108A ILE* 2.8 50.0 + - + +
132A ILE 4.0 5.6 - - - +
133A ILE* 3.8 28.7 - - + -
134A PRO* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.0 5.4 - - - -
76A LYS* 2.6 38.9 + - + -
77A ASP* 3.0 43.8 + - + +
79A ASN* 5.0 7.9 - - - +
100A LYS* 5.5 5.8 - - + +
101A ILE* 1.3 72.9 - - - +
103A THR* 1.3 59.6 + - - +
107A ASN* 3.3 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.1 25.5 + - + +
74A GLY 3.4 7.0 - - - -
75A VAL* 4.0 9.6 - - + -
76A LYS* 5.0 3.4 - - - -
101A ILE* 3.8 22.4 - - + +
102A LYS* 1.3 79.9 - - - +
104A ASN* 1.3 60.1 + - - +
105A TYR* 3.1 16.8 + - - +
106A GLY* 2.7 42.0 + - - +
107A ASN* 4.9 0.9 - - - +
108A ILE* 4.6 13.7 - - + -
314A ILE* 3.7 3.9 - - + +
----------------------------------------------------------
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