Contacts of the strand formed by residues 73 - 79 (chain n) in PDB entry 5GJQ
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 73 (chain n).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68n ASN* 3.9 1.6 - - - -
69n VAL* 2.9 31.5 + - + -
70n ASP* 2.9 24.9 + - + +
71n ARG 3.6 0.2 - - - -
72n HIS* 1.3 112.3 - - + +
74n GLY* 1.3 70.1 + - - +
106n ILE 5.0 0.9 - - - +
108n LEU* 3.6 34.1 - - + -
111n LEU* 3.8 22.9 - - + -
137n LEU* 4.2 6.1 - - + -
138n GLY 3.3 2.7 - - - +
139n SER* 3.9 0.7 - - - +
224n HIS* 4.0 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47n PHE* 4.2 5.2 - - - -
67n PHE 3.4 7.6 - - - -
73n VAL* 1.3 77.2 - - - +
75n MET* 1.3 62.2 + - - +
137n LEU* 3.2 5.4 - - - -
138n GLY 2.9 34.3 + - - -
224n HIS* 3.3 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47n PHE* 5.2 1.3 - - - -
65n ARG 3.7 0.7 - - - +
66n LEU* 3.2 6.8 - - - +
67n PHE* 2.7 45.1 + - + +
69n VAL* 3.7 30.1 - - + -
74n GLY* 1.3 74.4 - - - +
76n ALA* 1.3 62.3 + - - +
77n VAL* 3.7 21.8 - - + -
84n ALA 4.0 5.4 - - - +
87n LEU* 4.2 6.7 - - + +
88n ALA* 3.9 34.5 - - - +
91n ALA* 4.9 2.0 - - + -
135n PHE* 3.5 36.3 - - + -
136n MET 3.1 10.5 - - - +
137n LEU* 3.7 9.9 - - + -
224n HIS* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36n ALA* 5.2 3.6 - - + -
47n PHE* 3.9 24.9 - - + -
48n GLY 5.4 1.6 - - - +
49n VAL* 4.8 5.4 - - + -
65n ARG 3.4 5.4 - - - -
66n LEU* 3.5 19.3 - - + -
75n MET* 1.3 75.6 - - - +
77n VAL* 1.3 62.2 + - - +
135n PHE* 3.2 1.7 - - - -
136n MET* 2.7 49.6 + - + +
165n ILE* 4.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36n ALA* 4.0 8.7 - - - +
65n ARG* 3.1 42.4 + - + +
67n PHE* 3.8 21.5 - - + -
75n MET* 3.7 19.1 - - + -
76n ALA* 1.3 78.3 - - - +
78n ALA* 1.3 65.7 + - - +
81n LEU* 4.2 9.0 - - + -
84n ALA* 3.7 31.9 - - + -
133n CYS* 5.7 0.7 - - + -
134n SER 3.6 5.6 - - - +
135n PHE* 3.6 17.3 - - + -
165n ILE* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30n VAL* 3.9 7.1 - - + +
33n SER* 4.0 7.9 - - - +
34n SER 4.1 7.9 - - - +
36n ALA* 4.9 0.7 - - + -
65n ARG* 3.3 15.7 - - - +
77n VAL* 1.3 79.5 - - - +
79n GLY* 1.3 59.4 + - - +
84n ALA* 5.8 0.7 - - - -
133n CYS* 3.3 4.4 - - - -
134n SER 2.8 37.4 + - - -
165n ILE* 3.7 32.5 - - + +
166n GLY* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain n).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29n ALA 4.3 10.1 - - - -
30n VAL* 4.5 2.7 - - - -
33n SER* 3.1 27.9 + - - -
65n ARG* 4.0 7.8 + - - +
78n ALA* 1.3 74.8 - - - +
80n LEU* 1.3 66.8 + - - -
81n LEU* 3.0 9.6 + - - +
84n ALA* 5.9 0.4 - - - +
132n GLY 3.6 5.6 - - - -
133n CYS* 4.4 0.2 - - - -
----------------------------------------------------------
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