Contacts of the strand formed by residues 136 - 140 (chain A) in PDB entry 3GUU
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 TYR 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TRP 3.8 3.8 - - - +
77A ILE* 4.0 28.0 - - + +
78A PRO* 3.8 11.0 - - + -
81A PRO* 3.7 35.3 - - + +
82A ALA 4.9 0.7 - - - -
85A PRO* 4.0 26.1 - - + +
86A LYS 3.0 19.2 + - - +
87A ILE* 3.5 5.0 - - + -
88A PHE* 2.8 26.5 + - - +
134A GLY 4.7 1.8 - - - -
135A TYR* 1.3 72.0 - - - +
137A VAL* 1.3 62.6 + - - +
166A LEU* 3.9 20.0 - - + -
170A GLN* 3.9 30.1 + - + -
172A LEU* 3.9 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.1 8.5 - - - +
76A TRP* 2.9 49.1 + - + +
88A PHE* 3.4 17.9 - - + +
90A TYR* 4.8 2.0 - - + -
127A ILE* 3.8 29.2 - - + -
130A ALA* 3.8 28.3 - - + -
131A LEU* 3.8 18.8 - - + -
135A TYR 3.8 8.3 - - - +
136A TYR* 1.3 78.8 - - - +
138A VAL* 1.3 69.0 + - - +
166A LEU* 4.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 4.2 4.9 - - + -
74A THR 3.4 8.7 - - - +
75A VAL* 3.9 10.1 - - + -
87A ILE* 4.1 12.3 - - + -
88A PHE 3.0 4.5 + - - +
89A SER* 3.3 26.9 + - - +
90A TYR 3.0 24.6 + - - -
136A TYR 4.2 0.4 - - - -
137A VAL* 1.3 78.3 - - - +
139A SER* 1.3 64.4 + - - +
140A SER* 4.1 11.9 - - - +
162A GLY 3.7 23.8 - - - +
163A ILE* 3.8 16.8 - - + -
166A LEU* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.7 0.2 - - - -
74A THR* 2.9 31.7 + - - -
76A TRP* 4.1 9.4 - - - -
89A SER* 5.4 0.4 - - - -
90A TYR* 2.8 25.5 + - - -
92A VAL* 4.0 7.1 + - - +
103A PRO* 4.7 0.5 - - - +
107A TYR* 2.6 43.6 + - - -
127A ILE* 5.0 0.4 - - - -
138A VAL* 1.3 75.1 - - - +
140A SER* 1.3 65.9 + - - +
141A ASP* 4.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.4 14.2 + - - -
73A ALA* 3.7 10.9 - - - +
89A SER* 5.5 2.7 + - - -
90A TYR 4.5 2.1 + - - +
91A GLN* 5.3 3.1 + - - -
92A VAL 5.8 0.2 + - - -
103A PRO* 4.1 8.5 - - - +
138A VAL* 4.1 4.8 - - - +
139A SER* 1.3 77.1 + - - +
141A ASP* 1.3 62.9 + - - +
142A HIS* 3.0 22.2 + - - -
158A ALA 3.7 7.9 + - - -
159A ILE* 4.1 18.3 + - - +
162A GLY* 3.4 28.6 - - - -
----------------------------------------------------------
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