Contacts of the strand formed by residues 73 - 83 (chain A) in PDB entry 1VPF
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 GLU 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO* 3.7 24.9 - - + +
71A THR 5.5 0.2 - - - -
72A GLU* 1.3 85.4 - - - +
74A SER* 1.3 63.0 + - - +
97A LEU* 3.7 34.3 - - + +
98A GLN 3.2 14.6 - - - +
99A HIS* 3.8 10.3 + - + -
100A ASN* 3.2 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 1.3 73.7 - - - +
75A ASN* 1.3 64.4 + - - +
97A LEU* 3.6 8.0 - - - +
98A GLN* 2.7 42.2 + - - +
100A ASN* 2.4 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 1.3 81.5 - - - +
76A ILE* 1.3 62.8 + - - +
77A THR* 5.5 1.3 - - - +
95A SER* 4.3 15.1 - - - +
96A PHE 3.3 24.9 + - - +
97A LEU* 3.9 16.7 - - - +
98A GLN* 5.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.5 29.6 - - + -
75A ASN* 1.3 74.4 - - - +
77A THR* 1.3 65.2 + - - +
78A MET* 3.8 22.4 - - + -
94A MET 3.7 0.7 - - - +
95A SER* 3.2 4.2 - - - -
96A PHE* 2.9 45.9 + - + +
98A GLN* 3.9 23.3 - - + +
14B VAL* 6.3 0.7 - - - +
15B VAL* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 5.5 1.4 - - - +
76A ILE* 1.3 74.8 - - - +
78A MET* 1.3 66.4 + - - +
93A GLU* 3.6 29.6 - - + +
94A MET 3.4 7.0 - - - +
95A SER* 2.8 19.2 + - - +
14B VAL* 3.2 33.5 - - + +
15B VAL* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.9 16.4 - - - -
53A PRO* 3.5 34.5 - - + +
54A LEU* 3.9 9.9 - - + -
76A ILE* 3.8 22.7 - - + -
77A THR* 1.3 81.6 - - - +
79A GLN* 1.3 63.8 + - - +
80A ILE* 3.4 11.0 + - + +
93A GLU* 3.2 3.7 - - - -
94A MET 2.8 33.8 + - - +
96A PHE* 4.1 11.0 - - + -
98A GLN* 5.5 0.7 - - - +
14B VAL* 4.2 3.8 - - - -
15B VAL* 3.6 22.7 - - + +
20B VAL* 3.8 27.8 - - + -
23B ARG* 4.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 1.3 69.1 - - - +
80A ILE* 1.3 65.1 - - - +
91A ILE* 4.5 15.3 - - + +
92A GLY 3.1 10.8 - - - +
93A GLU* 5.0 7.0 + - + +
14B VAL* 3.7 15.3 - - + +
15B VAL 2.9 16.1 + - - +
16B LYS* 3.4 28.8 - - - +
17B PHE* 2.9 53.7 + - + +
20B VAL* 4.1 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.7 14.8 - - + -
47A PHE* 3.7 22.2 - - + -
48A LYS 3.8 7.4 - - - +
49A PRO* 4.1 8.1 - - + +
52A VAL* 3.8 27.4 - - + -
78A MET* 3.4 15.5 + - + +
79A GLN* 1.3 81.1 - - - +
81A MET* 1.3 76.6 + - - +
82A ARG* 4.1 2.4 + - - +
91A ILE* 3.6 1.1 - - - -
92A GLY 2.9 30.8 + - - +
94A MET* 3.7 27.7 - - + +
96A PHE* 4.5 2.0 - - + -
20B VAL* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE 4.5 0.2 - - - -
47A PHE* 3.2 4.3 - - - -
48A LYS* 2.8 56.3 + - + +
80A ILE* 1.3 76.4 - - - +
82A ARG* 1.3 60.0 + - - +
83A ILE* 4.9 0.7 - - - -
89A GLN* 3.3 39.7 - - + +
90A HIS 3.2 12.3 - - - +
91A ILE* 3.7 27.4 - - + -
17B PHE* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.4 19.4 + - - -
45A TYR* 3.2 53.9 + - + -
46A ILE 3.4 7.0 - - - +
47A PHE* 3.5 29.6 - - + -
80A ILE 4.1 2.9 + - - +
81A MET* 1.3 73.4 - - - +
83A ILE* 1.3 62.2 + - - +
84A LYS* 5.7 0.6 - - - +
88A GLY 4.2 0.5 - - - +
90A HIS* 3.1 48.9 + - + +
92A GLY 5.9 2.2 - - - +
94A MET* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 4.9 1.8 - - - -
46A ILE* 2.9 71.0 + - + +
48A LYS* 4.9 10.5 - - + -
81A MET 4.8 2.5 - - - +
82A ARG* 1.3 76.7 - - - +
84A LYS* 1.3 73.1 + - - +
85A PRO* 3.6 0.9 - - - +
86A HIS* 5.4 2.2 - - - +
87A GLN 5.1 0.4 - - - +
88A GLY 3.2 31.6 - - - +
89A GLN* 3.0 40.4 - - + +
----------------------------------------------------------
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