Contacts of the strand formed by residues 125 - 134 (chain B) in PDB entry 3KDH
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 LYS 125 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 6.1 0.4 - - - +
112B PHE 3.6 9.0 - - - +
113B ARG* 3.2 49.0 - - + +
123B ASN* 3.5 19.3 - - - +
124B TYR* 1.3 83.1 - - - +
126B SER* 1.3 60.1 + - - +
127B VAL* 5.9 0.4 - - + -
149B TYR* 3.1 6.9 - - - +
150B THR* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU 3.9 0.7 + - - +
111B SER* 3.2 7.8 + - - -
112B PHE* 3.0 66.3 + - - -
124B TYR* 3.9 11.4 - - - -
125B LYS* 1.3 74.3 - - - +
127B VAL* 1.3 64.9 + - - +
128B THR* 3.8 9.5 + - - -
147B GLU* 3.3 22.8 + - - +
148B SER 3.3 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.5 26.2 - - + +
26B HIS* 3.3 13.3 - - + -
102B PHE* 6.1 0.2 - - + -
109B VAL* 3.8 25.8 - - + -
110B LEU 3.5 4.3 - - - +
111B SER* 3.9 15.9 - - - +
126B SER* 1.3 77.9 + - - +
128B THR* 1.3 64.5 + - - +
147B GLU* 3.3 1.2 - - - -
148B SER* 2.9 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 4.2 0.7 - - - -
51B TRP* 4.9 0.7 - - - -
54B ILE* 3.8 33.0 - - + -
63B TYR* 5.0 4.7 + - - +
108B ARG 3.8 0.5 - - - +
109B VAL* 3.2 4.5 - - - +
110B LEU* 2.8 40.0 + - - +
112B PHE* 5.7 1.0 - - - -
126B SER* 3.8 5.5 + - - -
127B VAL* 1.3 76.3 - - - +
129B SER* 1.3 65.4 + - - +
130B VAL* 4.7 0.4 - - + -
145B VAL* 3.6 27.1 - - + -
146B LEU 3.2 4.0 - - - +
147B GLU* 3.5 26.1 + - - +
174B LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.6 12.9 - - - +
25B TYR* 5.3 0.4 - - - -
26B HIS* 2.9 26.9 + - - -
107B HIS 5.1 0.7 - - - -
108B ARG 3.3 7.6 - - - -
109B VAL* 4.0 16.2 - - - -
128B THR* 1.3 73.5 - - - +
130B VAL* 1.3 66.0 + - - +
131B ASN* 3.0 20.6 + - - -
145B VAL* 3.3 8.3 - - - +
146B LEU* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.0 18.4 - - + -
50B VAL* 4.0 12.3 - - + -
51B TRP* 3.8 20.2 - - + +
54B ILE* 3.5 32.5 - - + -
107B HIS 3.7 4.9 - - - +
108B ARG* 2.9 38.7 + - + +
128B THR* 4.7 0.4 - - + -
129B SER* 1.3 79.7 - - - +
131B ASN* 1.3 67.2 + - - +
132B GLU 4.3 1.1 + - - -
143B THR* 3.6 22.9 - - + -
144B VAL 3.9 1.8 - - - -
145B VAL* 4.4 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 24.8 - - + +
21B VAL* 3.6 21.6 - - - +
47B ALA* 5.0 0.4 - - - -
107B HIS 4.9 3.5 - - - +
129B SER* 3.0 31.8 + - - -
130B VAL* 1.3 80.0 - - - +
132B GLU* 1.3 62.5 + - - +
133B PHE* 3.6 7.0 - - + -
143B THR* 3.3 6.0 - - - -
144B VAL 2.8 51.3 + - - +
146B LEU* 3.8 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.5 10.2 - - - +
47B ALA* 2.8 42.4 + - + +
48B SER* 4.3 1.7 + - - -
108B ARG* 5.0 8.3 + - - +
130B VAL 4.3 0.6 + - - -
131B ASN* 1.3 73.6 - - - +
133B PHE* 1.3 77.9 + - - +
134B LEU* 4.4 1.7 + - - +
141B VAL* 4.1 20.6 - - + +
142B TYR 3.5 11.7 - - - +
143B THR* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.8 21.3 - - + -
17B THR* 3.9 27.6 - - + -
18B LEU* 3.8 35.2 - - + -
131B ASN* 3.6 12.8 - - + -
132B GLU* 1.3 83.4 - - - +
134B LEU* 1.3 61.5 + - - +
135B ASN 3.8 0.9 + - - -
141B VAL* 3.2 6.2 - - - +
142B TYR* 2.8 69.9 + + + +
144B VAL* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 4.3 1.7 + - - +
133B PHE* 1.3 73.5 - - - +
135B ASN* 1.3 72.8 + - - +
136B GLN* 3.4 34.6 + - - +
139B GLY* 3.6 26.2 - - - +
140B LYS 3.7 2.9 - - - +
141B VAL* 4.0 13.7 - - + -
----------------------------------------------------------
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