Contacts of the strand formed by residues 93 - 102 (chain A) in PDB entry 1MS4
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 ARG 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP 3.5 20.1 + - - -
60A ASN* 3.3 30.7 + - - +
61A SER 3.3 16.2 - - - +
63A ILE* 3.6 16.2 - - + -
85A ASN* 3.6 7.0 - - - +
91A VAL* 3.0 21.3 + - - +
92A SER* 1.3 75.1 - - - +
94A VAL* 1.3 59.2 + - - +
95A VAL* 3.7 16.9 - - + +
111A GLY 3.8 0.2 - - - +
112A SER* 3.4 4.0 + - - -
113A TYR* 2.8 68.6 + - + +
115A SER 5.0 0.2 - - - -
116A SER* 2.9 43.6 + - - +
118A SER 3.7 7.3 + - - -
120A TRP* 5.2 2.4 - - - +
123A HIS* 4.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 4.2 1.7 - - - +
63A ILE* 3.4 33.0 + - - +
64A ASP* 3.9 0.4 - - - -
65A THR* 3.7 22.1 + - - +
83A ILE* 3.7 24.0 - - + +
84A LYS 4.1 6.7 - - - +
85A ASN* 3.8 15.9 - - - +
93A ARG* 1.3 71.4 - - - +
95A VAL* 1.3 64.3 - - - +
110A VAL* 3.7 22.4 - - + -
111A GLY 3.1 11.0 - - - +
112A SER* 3.9 15.9 - - - +
132A LEU* 4.4 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
51A ASP* 4.4 3.8 - - - +
59A ASP 5.3 0.9 - - - +
63A ILE* 4.5 9.0 - - + -
93A ARG* 3.7 39.3 - - + +
94A VAL* 1.3 81.4 - - - +
96A ASP* 1.3 76.7 + - + +
97A PRO* 3.3 6.3 - - - -
110A VAL* 3.2 6.2 - - - +
111A GLY* 2.9 41.0 + - - +
113A TYR* 3.8 22.0 - - + -
176A LEU* 4.4 10.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
36A LEU* 3.2 34.9 - - - +
53A ARG* 5.4 0.9 + - - -
95A VAL* 1.3 83.1 - - + +
97A PRO* 1.3 75.6 - - - +
98A THR* 3.0 14.2 + - - -
109A LEU 3.6 3.1 - - - +
110A VAL* 4.8 0.2 - - - -
119A TYR* 4.4 13.6 + - - -
176A LEU* 3.7 18.0 - - + +
177A GLY* 4.2 12.2 + - - +
179A ALA* 3.9 8.4 - - + -
195A GLN* 3.2 25.3 + - - -
230A GLU* 4.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.1 16.4 - - + +
38A ALA* 4.8 1.6 - - - +
49A ILE* 4.2 11.0 - - + -
50A ALA 4.4 9.9 - - - -
51A ASP* 3.3 21.3 - - - +
65A THR* 3.9 26.5 - - + +
94A VAL 5.2 0.2 - - - +
95A VAL* 3.3 4.4 - - - -
96A ASP* 1.3 89.8 - - - +
98A THR* 1.3 59.1 + - - +
99A VAL* 4.3 2.9 - - - +
108A VAL* 4.2 5.4 - - + -
109A LEU 3.3 9.4 - - - +
110A VAL* 3.4 15.7 - - + -
179A ALA* 3.8 0.7 - - - +
180A GLY* 3.4 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP 3.0 8.0 + - - -
97A PRO* 1.3 72.4 - - - +
99A VAL* 1.3 63.0 + - - +
108A VAL* 3.3 1.6 - - - -
109A LEU* 2.7 37.5 + - - +
177A GLY* 3.3 13.2 - - - -
178A GLY* 4.2 6.1 - - - +
179A ALA 3.0 33.9 + - - +
180A GLY 3.4 11.0 - - - +
181A VAL 4.9 0.2 - - - -
182A ALA* 4.3 10.3 - - + +
192A TYR* 3.2 33.8 + - + -
193A PRO* 5.3 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.9 25.1 - - + +
40A VAL* 4.2 19.7 - - + -
49A ILE* 3.9 31.0 - - + -
97A PRO 4.7 0.4 - - - +
98A THR* 1.3 80.0 - - - +
100A ILE* 1.3 73.7 + - - +
106A LEU* 4.2 22.2 - - + -
107A TYR 3.2 7.0 - - - +
108A VAL* 4.5 6.7 - - + -
180A GLY 3.0 8.7 + - - +
181A VAL* 3.4 7.8 - - - +
182A ALA 2.8 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 1.3 79.2 - - - +
101A VAL* 1.3 69.4 + - - +
102A LYS 4.5 0.2 - - - +
105A LYS 3.7 1.2 - - - +
106A LEU* 3.8 2.1 - - - -
107A TYR* 2.9 41.8 + - + +
181A VAL* 5.3 0.4 - - - -
182A ALA* 3.6 18.4 - - + -
183A ILE* 3.6 24.2 - - - +
184A VAL* 3.8 26.2 - - + -
190A LEU* 4.2 18.8 - - + -
191A VAL 3.6 22.0 - - - +
192A TYR* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.6 40.4 - - + -
41A ASN 3.8 11.7 - - - +
42A VAL* 3.7 26.7 - - + -
43A ASP 5.6 0.2 - - - +
99A VAL* 4.6 0.9 - - + -
100A ILE* 1.3 79.8 - - - +
102A LYS* 1.3 62.6 + - - +
103A GLY 3.9 14.1 - - - +
105A LYS 3.4 4.9 - - - +
106A LEU* 4.1 4.9 - - + -
181A VAL* 5.8 1.2 - - + +
182A ALA 5.3 1.0 + - - -
183A ILE* 5.8 0.4 - - - +
184A VAL* 3.2 17.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
100A ILE* 4.1 1.2 + - - +
101A VAL* 1.3 73.9 - - - +
103A GLY* 1.3 63.3 + - - +
104A ASN 3.2 0.3 + - - -
105A LYS* 2.9 35.5 + - - +
107A TYR* 4.2 16.7 - - + +
184A VAL* 3.8 23.3 - - + -
188A GLY* 2.6 32.1 + - - -
190A LEU* 3.7 21.1 - - + +
213A GLU* 2.7 35.4 + - - +
----------------------------------------------------------
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