Contacts of the helix formed by residues 93 - 103 (chain A) in PDB entry 2H5X
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 ASP 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 3.9 6.4 + - - +
90A ALA 5.5 1.4 - - - +
91A VAL 4.8 2.6 - - - +
92A HIS* 1.3 74.4 - - - +
94A ALA* 1.3 58.4 + - - +
95A PRO* 3.8 12.8 - - + +
96A ALA* 3.0 15.7 + - - +
97A LEU* 2.7 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 4.0 29.6 - - + +
70A LEU* 3.8 24.2 - - + -
89A LEU* 4.3 7.9 - - + +
92A HIS 3.6 0.6 + - - -
93A ASP* 1.3 69.6 - - - +
95A PRO* 1.3 65.0 - - + +
97A LEU* 3.1 0.9 + - - +
98A ARG* 2.7 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.4 13.9 - - + +
94A ALA* 1.3 96.5 - - + +
96A ALA* 1.3 59.9 + - - +
98A ARG* 3.7 12.0 + - - +
99A GLN* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 4.5 8.3 - - + -
93A ASP* 3.0 26.4 + - - +
95A PRO* 1.3 77.2 - - - +
97A LEU* 1.3 68.6 + - - +
99A GLN* 2.8 10.1 + - - +
100A VAL* 2.7 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.6 6.7 - - + -
74A LEU* 3.9 26.0 - - + -
88A ALA* 4.2 17.5 - - + +
89A LEU* 3.5 27.8 - - + -
92A HIS* 3.7 26.1 - - + +
93A ASP 2.7 20.7 + - - +
94A ALA* 3.6 4.9 - - - +
96A ALA* 1.3 72.6 - - - +
98A ARG* 1.3 65.9 + - - +
100A VAL* 3.3 4.8 + - - +
101A LEU* 3.0 31.0 + - + +
109A LEU* 4.0 25.4 - - + -
112A VAL* 5.7 1.1 - - + -
123A MET* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.1 43.2 + - - +
67A THR* 4.3 1.6 - - - +
70A LEU* 3.9 29.5 - - + +
94A ALA* 2.7 32.1 + - - +
95A PRO* 3.7 8.8 - - - +
97A LEU* 1.3 72.0 - - - +
99A GLN* 1.3 66.6 + - - +
101A LEU* 2.8 21.3 + - - +
102A ALA* 3.2 10.4 + - - +
131A VAL* 3.3 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO 3.1 11.9 + - - +
96A ALA* 2.8 17.3 + - - +
98A ARG* 1.3 74.1 - - - +
100A VAL* 1.3 65.1 + - + +
102A ALA* 2.8 18.3 + - - +
103A ASP* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 3.9 14.6 - - - +
96A ALA* 2.7 24.6 + - + +
97A LEU* 3.5 7.0 - - - +
99A GLN* 1.3 71.8 - - + +
101A LEU* 1.3 57.0 + - - +
103A ASP* 3.2 2.4 + - - -
104A GLY* 2.9 25.6 + - - -
105A ASN* 3.0 51.1 + - + +
108A ALA* 3.8 19.3 - - + -
109A LEU* 3.5 24.9 - - + -
124A VAL* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.3 4.0 - - + -
74A LEU* 4.4 16.8 - - + -
97A LEU* 3.0 26.7 + - + +
98A ARG* 2.8 16.3 + - - +
100A VAL* 1.3 71.1 - - - +
102A ALA* 1.3 56.6 + - - +
104A GLY* 4.1 2.0 - - - +
109A LEU* 3.8 31.2 - - + -
123A MET* 4.3 6.1 - - + -
124A VAL* 4.2 21.3 - - + +
127A LEU* 3.5 36.3 - - + +
128A ARG* 2.8 33.6 - - - +
131A VAL* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG 3.2 6.1 + - - +
99A GLN* 2.8 11.9 + - - +
101A LEU* 1.3 77.3 - - - +
103A ASP* 1.3 66.7 + - - +
104A GLY* 2.8 10.2 + - - -
128A ARG* 4.5 15.7 - - - +
133A VAL* 4.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLN* 2.9 26.9 + - - +
100A VAL* 4.0 2.9 + - - +
102A ALA* 1.3 79.8 - - - +
104A GLY* 1.3 52.6 + - - +
105A ASN* 2.7 28.5 + - + +
----------------------------------------------------------
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