Contacts of the strand formed by residues 60 - 65 (chain B) in PDB entry 3T30
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 HIS 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.7 23.0 - - + +
55B ALA* 4.0 8.6 - - + +
56B LYS 3.8 20.2 - - - -
58B GLU* 2.7 38.3 + - - -
59B MET* 1.3 78.1 - - - +
61B ARG* 1.3 62.8 + - - +
62B VAL* 5.6 1.3 - - + -
82B SER* 3.2 5.5 - - - -
83B LEU* 2.7 40.6 + - + +
85B ALA 5.8 0.2 - - - -
106B LEU* 4.2 1.8 - - + -
108B ALA 3.2 6.7 - - - +
109B GLY* 3.8 9.0 - - - -
110B SER* 3.5 3.2 + - - -
111B GLY* 2.9 34.0 + - - -
113B VAL* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 3.9 4.7 - - + -
60B HIS* 1.3 77.5 - - - +
62B VAL* 1.3 63.4 + - - +
63B GLU* 4.0 14.9 + - + -
79B THR* 2.8 48.6 + - + +
81B ALA 3.3 10.5 - - - +
82B SER* 3.8 8.3 - - - +
106B LEU* 3.6 3.2 - - - +
107B ARG* 2.8 64.3 + - + +
108B ALA* 3.0 16.2 + - + +
52C GLY* 4.4 1.7 - - - -
53C GLU* 2.7 47.6 + - - +
114C PHE* 3.5 34.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.2 16.8 - - + -
49B ILE* 4.5 9.9 - - + -
60B HIS* 5.6 0.9 - - + -
61B ARG* 1.3 79.0 - - - +
63B GLU* 1.3 68.8 + - - +
79B THR* 3.6 3.6 - - - +
80B ILE* 2.9 45.4 + - + +
81B ALA* 3.0 18.9 + - + +
83B LEU* 6.0 1.1 - - + -
104B PHE* 4.5 7.6 - - + -
105B GLN 3.4 9.4 - - - +
106B LEU* 4.1 12.1 - - + -
113B VAL* 4.1 26.0 - - + -
115B LEU* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 4.0 8.8 + - - -
62B VAL* 1.3 78.6 - - - +
64B ILE* 1.3 63.2 + - - +
65B LEU* 3.7 10.2 - - + +
77B PRO* 3.2 29.2 - - + +
78B VAL 3.1 18.4 - - - +
79B THR* 4.1 5.7 + - - +
80B ILE* 4.3 0.7 - - - +
104B PHE* 3.4 4.2 - - - -
105B GLN* 2.9 50.5 + - + +
107B ARG* 3.3 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 5.7 0.2 - - + -
63B GLU* 1.3 75.3 - - - +
65B LEU* 1.3 71.3 + - - +
66B PRO* 4.1 0.3 - - - +
76B GLN 4.6 0.2 - - - +
77B PRO* 3.4 3.6 - - - +
78B VAL* 2.7 35.8 + - - +
80B ILE* 3.7 29.4 - - + -
98B LEU* 3.9 32.8 - - + -
102B VAL* 3.8 14.4 - - + -
103B THR 3.3 9.4 - - - +
104B PHE* 3.9 18.4 - - + -
18C LEU* 3.4 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 5.1 4.3 - - + -
63B GLU* 3.7 8.5 - - + +
64B ILE* 1.3 82.6 - - - +
66B PRO* 1.3 77.8 - - + +
67B PRO 4.2 5.0 - - - -
77B PRO* 3.6 31.4 - - + -
102B VAL* 5.5 0.5 - - - -
103B THR* 2.8 42.2 + - + +
105B GLN* 3.2 42.8 - - + +
18C LEU* 6.2 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