Contacts of the strand formed by residues 88 - 97 (chain G) in PDB entry 3V5I
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 VAL 88 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G LEU* 4.1 9.0 - - + -
60G ILE* 3.4 20.2 - - + +
62G LEU* 4.0 19.5 - - + -
81G ILE* 3.9 38.9 - - + +
84G ILE* 3.9 28.3 - - + -
86G PRO 3.6 2.6 + - - +
87G ASP* 1.3 77.6 - - - +
89G GLN* 1.3 71.4 - - - +
90G THR* 4.5 2.0 - - + -
107G GLY* 3.3 4.7 - - - -
108G ALA* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ASP* 3.6 19.4 + - + +
60G ILE 2.7 18.1 + - - +
61G TYR* 3.5 37.1 + - + -
62G LEU* 2.8 29.5 + - - +
88G VAL* 1.3 72.7 - - - +
90G THR* 1.3 61.5 + - - +
91G ILE* 4.8 5.1 - - + +
111G LYS* 3.3 46.2 - - + +
113G PHE* 3.2 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G LEU* 3.3 18.4 - - + -
64G ILE* 4.1 13.2 - - + -
81G ILE* 5.3 1.6 - - + -
88G VAL* 3.7 5.1 + - + +
89G GLN* 1.3 76.8 - - - +
91G ILE* 1.3 60.1 + - - +
103G LEU 3.8 14.8 - - - +
104G LEU* 2.7 31.4 + - - +
106G ALA 4.9 0.4 - - - -
107G GLY* 3.7 17.9 - - - -
111G LYS 3.1 4.8 + - - +
112G ARG* 3.4 13.3 - - - +
113G PHE 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G TYR* 4.3 24.9 - - + -
62G LEU 2.9 10.6 + - - +
63G TYR* 3.3 55.0 - - + +
64G ILE* 2.8 25.9 + - - +
89G GLN* 4.8 5.2 - - + +
90G THR* 1.3 79.7 - - - +
92G CYS* 1.3 60.6 + - - +
93G ILE* 3.5 10.9 + - + -
104G LEU* 4.4 1.8 - - - -
113G PHE* 3.5 24.7 - - + +
115G LEU* 4.3 6.5 - - + -
190G MET* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ILE* 3.4 9.0 - - + +
91G ILE* 1.3 70.5 - - - +
93G ILE* 1.3 63.2 + - - +
95G MET 3.9 2.9 - - - -
96G ALA* 3.6 36.8 - - + -
104G LEU* 3.7 28.8 - - + +
113G PHE 2.9 13.3 + - - +
114G ALA* 3.9 6.1 - - + -
115G LEU* 3.0 25.8 + - - +
118G ALA* 3.3 20.5 - - - +
119G GLU 3.8 6.1 - - - -
120G VAL* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASN* 5.1 3.8 - - - +
45F VAL* 3.9 35.9 - - + -
76F ALA* 4.1 13.5 - - + -
80F THR* 4.6 3.8 - - - +
31G MET* 4.4 13.2 - - + -
63G TYR* 4.0 25.4 - - + -
64G ILE 3.1 10.7 + - - +
65G ASN* 3.1 33.0 - - + +
91G ILE* 3.5 2.2 + - + -
92G CYS* 1.3 78.1 - - - +
94G GLY* 1.3 61.7 + - - +
95G MET 3.1 4.2 + - - -
115G LEU* 3.6 31.2 - - + -
118G ALA* 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F THR* 3.5 31.0 - - - +
75F PHE* 4.8 4.0 + - - +
76F ALA* 3.8 14.5 - - - +
79F ASP* 5.8 1.0 + - - +
65G ASN* 3.8 4.9 - - - -
93G ILE* 1.3 69.1 - - - +
95G MET* 1.3 59.6 + - - +
115G LEU* 5.9 0.2 - - - +
117G ASN 4.4 1.6 - - - +
118G ALA* 3.3 12.5 - - - +
119G GLU* 2.8 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F THR* 4.0 23.8 - - + +
142F HIS* 4.7 2.9 - - + -
64G ILE 3.9 0.2 - - - +
65G ASN* 3.1 12.1 + - - +
66G SER 2.9 30.9 + - - +
67G PRO* 5.2 2.7 - - + -
92G CYS* 3.9 3.6 - - - -
93G ILE 3.1 4.2 + - - -
94G GLY* 1.3 75.4 - - - +
96G ALA* 1.3 64.2 + - - +
97G ALA* 4.1 25.6 - - + +
119G GLU* 3.0 52.3 - - + +
120G VAL 4.3 1.1 - - - -
121G MET* 4.3 6.7 - - + -
174G PHE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ILE* 4.2 10.1 - - + -
66G SER 3.5 3.8 - - - +
92G CYS* 3.6 19.5 - - + -
95G MET* 1.3 74.6 - - - +
97G ALA* 1.3 59.3 + - - +
100G GLY* 4.0 7.0 - - - +
101G SER* 3.3 28.6 - - - +
104G LEU* 4.2 11.2 - - + -
119G GLU 2.8 10.4 + - - +
120G VAL* 3.3 3.0 - - + -
121G MET 3.1 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G SER 2.9 7.7 + - - +
67G PRO* 3.4 28.2 - - + +
68G GLY* 3.4 1.2 - - - -
95G MET* 4.1 13.9 - - + -
96G ALA* 1.3 74.4 - - - +
98G ALA* 1.3 62.9 + - - +
99G MET 3.3 0.2 + - - -
100G GLY* 2.8 24.6 + - - -
101G SER 3.7 0.6 - - - +
121G MET* 3.4 30.7 - - + +
----------------------------------------------------------
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