Contacts of the strand formed by residues 126 - 132 (chain A) in PDB entry 4DVH
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 126 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 4.1 3.1 - - - -
124A GLY 3.8 3.0 + - - -
125A SER* 1.3 74.9 - - - +
127A TRP* 1.3 65.1 + - - -
145A THR 3.2 13.2 - - - -
147A ASN 3.9 6.7 - - - -
163A ASP* 3.5 0.2 - - - +
164A VAL* 2.8 37.6 + - - +
165A TRP* 3.4 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 2.9 26.7 + - - -
78A ASN* 3.4 56.0 - - + +
79A HIS* 3.5 24.2 - + - -
82A TYR* 3.7 12.1 - - + -
122A ASN* 2.9 15.9 + - - +
126A GLY* 1.3 74.8 - - - -
128A THR* 1.3 60.1 + - - +
129A TRP* 3.2 24.7 - + + +
144A ASN* 3.5 0.3 - - - -
145A THR* 2.9 32.2 + - - +
147A ASN 3.1 20.7 + - - -
149A GLY 4.0 0.7 - - - -
161A ALA* 4.4 10.1 - - + -
162A VAL 3.4 9.9 - - - -
163A ASP* 3.5 50.0 - - + -
164A VAL* 4.3 0.9 - - - -
165A TRP* 3.6 3.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.3 52.3 - - + +
118A ALA* 3.9 10.1 - - + -
119A GLY* 3.3 20.0 - - - +
122A ASN* 3.6 4.3 + - - -
127A TRP* 1.3 72.3 - - - +
129A TRP* 1.3 62.3 + - - +
142A ILE* 4.2 4.3 - - + -
143A ASP 3.6 2.5 - - - -
144A ASN* 2.7 23.3 + - - +
161A ALA* 3.6 1.0 - - - -
162A VAL* 2.8 35.1 + - - -
164A VAL* 4.3 5.3 - - - +
181A LEU* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.3 6.7 - + - -
78A ASN* 3.2 44.6 - - + -
81A PHE* 4.3 7.9 - + + -
115A PHE* 3.7 5.6 - - - -
127A TRP* 3.2 17.3 - + + +
128A THR* 1.3 77.6 - - - +
130A LEU* 1.4 57.9 + - - +
131A CYS* 3.7 15.5 - - - -
142A ILE* 3.3 9.9 - - - +
143A ASP* 2.8 49.4 + - + +
145A THR* 3.0 29.2 + - + -
149A GLY 4.3 0.7 - - - -
151A PRO* 3.3 27.4 - - + +
158A PRO* 3.6 34.5 - - + -
160A LEU 3.2 8.3 - - - -
161A ALA* 3.4 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 5.1 0.9 - - + -
101A VAL* 4.4 17.5 - - + -
105A PHE* 3.8 23.6 - - + -
111A PHE* 3.6 39.7 - - + -
115A PHE* 3.9 3.9 - - + -
129A TRP* 1.4 72.1 - - - +
131A CYS* 1.3 61.3 + - - +
140A LEU* 4.0 19.7 - - + -
141A VAL 3.4 13.7 - - - +
142A ILE* 4.3 1.6 - - + -
159A VAL* 2.9 43.2 + - + +
160A LEU* 2.9 26.7 + - + +
190A TRP* 5.2 2.0 - - + -
193A VAL* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TRP* 3.7 22.9 - - - -
130A LEU* 1.3 77.9 - - - +
132A VAL* 1.3 62.3 + - - +
140A LEU* 3.3 8.5 - - - +
141A VAL* 2.9 41.5 + - + +
143A ASP* 4.7 4.3 - - - -
151A PRO* 3.8 24.9 - - - -
156A LEU* 3.9 21.8 - - + -
157A ARG 3.3 9.9 - - - +
158A PRO* 3.8 13.0 - - - -
159A VAL* 4.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A CYS* 1.3 73.5 - - - +
133A ASP* 1.4 62.0 + - - +
134A PRO* 3.2 8.0 - - + +
138A ASN* 3.8 37.7 - - + +
139A GLN 3.5 3.4 - - - -
140A LEU* 3.9 10.3 - - + -
156A LEU* 3.8 3.1 - - - +
157A ARG* 2.9 36.9 + - + +
159A VAL* 4.1 6.5 - - + -
197A HIS* 3.6 28.3 - - + +
200A ALA* 3.9 30.5 - - + +
201A ILE* 4.1 6.7 - - + -
----------------------------------------------------------
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