Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 2HVY
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 GLY 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 1.3 75.5 - - - +
138A GLU* 1.3 65.6 + - - -
139A ILE* 3.4 4.0 + - - +
157A LYS* 4.4 4.0 - - - -
158A VAL* 2.7 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU 5.3 0.3 - - - +
137A GLY* 1.3 70.2 - - - -
139A ILE* 1.3 59.5 + - - +
155A THR* 3.1 28.1 + - - +
156A ARG* 3.8 6.1 - - - -
157A LYS* 3.1 48.8 + - + +
178A GLU* 4.8 0.5 - - - +
47B PRO* 3.4 6.6 - - - +
48B VAL* 3.0 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU 4.8 0.4 - - - +
135A PHE* 3.5 34.8 - - + +
136A GLU 4.9 0.4 - - - +
137A GLY 4.0 3.8 - - - +
138A GLU* 1.3 79.2 - - - +
140A ILE* 1.3 68.5 + - - +
141A GLN* 3.6 2.6 + - + -
155A THR* 3.3 5.6 - - - -
156A ARG* 2.9 49.4 + - + +
158A VAL* 3.7 24.0 - - + -
181A THR* 5.0 9.2 - - + -
186A LEU* 4.2 20.9 - - + -
46B GLY* 3.2 24.9 - - - +
47B PRO* 4.0 3.6 - - + -
48B VAL 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 1.3 77.0 - - - +
141A GLN* 1.3 62.3 + - - +
142A ARG 3.6 25.8 - - - +
143A PRO* 4.0 2.7 - - + -
153A LEU* 3.8 18.8 - - + -
154A ARG 4.0 4.0 - - - +
155A THR* 4.5 2.7 - - + +
189A HIS* 4.8 5.5 + - - -
23B VAL* 4.0 20.6 - - + -
44B VAL* 3.5 33.9 - - + +
45B PHE* 4.0 17.0 - - - +
46B GLY 2.9 16.1 + - - +
48B VAL* 4.2 17.5 - - + -
51B PRO* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.6 4.7 + - + +
140A ILE* 1.3 73.9 - - - +
142A ARG* 1.3 62.1 + - + +
143A PRO* 4.5 3.3 - - - +
154A ARG* 3.2 40.6 + - + +
155A THR 4.4 4.3 - - - -
156A ARG* 3.2 46.2 - - + +
180A GLY 3.2 19.2 + - - +
181A THR* 4.5 3.6 - - + +
182A TYR* 4.8 3.8 + - - +
185A SER* 5.5 3.1 + - - +
189A HIS* 5.4 9.1 - - - -
44B VAL 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.6 11.4 - - - +
141A GLN* 1.3 80.2 - - + +
143A PRO* 1.3 82.2 + - + +
144A PRO 3.8 0.9 - - - -
153A LEU* 4.1 3.3 - - - +
154A ARG* 3.4 45.3 + - + +
----------------------------------------------------------
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