Contacts of the strand formed by residues 130 - 143 (chain A) in PDB entry 1NKV
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 LEU 130 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 4.4 3.0 - - - +
104A CYS 3.2 17.3 - - - +
105A ASP 3.6 2.2 - - - +
107A ALA* 3.5 16.8 - - + +
126A LEU 3.4 11.2 + - - +
127A ALA* 4.1 18.1 + - - +
128A GLN 3.8 0.4 - - - -
129A SER* 1.3 76.3 - - - +
131A LYS* 1.3 75.5 - - - +
132A PRO* 3.5 1.0 - - - +
134A GLY* 3.4 31.9 - - - +
135A ILE 3.4 20.2 - - - +
136A MSE 3.8 25.4 - - + -
179A TYR* 5.4 7.6 - - + +
247A ALA* 6.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 4.7 10.4 - - - +
103A LYS* 3.5 40.9 - - + +
104A CYS* 3.1 14.8 + - - +
105A ASP* 3.1 44.1 + - - +
130A LEU* 1.3 81.4 - - - +
132A PRO* 1.3 81.0 - - + +
133A GLY 3.3 0.3 + - - -
134A GLY* 2.9 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 5.6 4.7 - - + -
130A LEU 3.5 1.3 - - - +
131A LYS* 1.3 91.7 - - + +
133A GLY* 1.3 63.0 + - - +
134A GLY* 3.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS 3.3 0.6 + - - -
132A PRO* 1.3 73.2 - - - +
134A GLY* 1.3 64.1 + - - +
135A ILE* 5.1 2.3 - - - +
246A ILE* 3.6 30.0 - - - +
247A ALA* 5.2 10.3 - - - +
204C ARG* 4.8 6.7 - - - -
205C ARG* 4.7 8.0 + - - -
208C GLU* 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.5 13.5 - - - -
130A LEU* 3.4 18.6 - - - +
131A LYS* 2.9 20.7 + - - -
132A PRO 3.0 1.1 - - - -
133A GLY* 1.3 82.5 - - - +
135A ILE* 1.3 63.8 + - - -
245A LEU 3.6 7.3 - - - +
246A ILE* 3.9 9.8 - - - +
247A ALA 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.2 35.4 - - + +
34A MSE 5.3 4.7 - - + -
105A ASP 3.0 10.8 + - - +
106A VAL* 2.9 40.3 - - + +
107A ALA 3.1 2.8 + - - -
130A LEU* 3.4 1.8 - - - +
133A GLY 5.1 1.8 - - - +
134A GLY* 1.3 73.9 - - - -
136A MSE 1.3 61.3 + - - +
137A LEU* 3.6 25.6 - - + -
182A VAL* 5.4 5.8 - - + -
244A ALA* 4.3 8.7 - - + -
245A LEU 3.4 8.7 - - - +
246A ILE* 5.3 6.1 - - + -
201C LEU* 5.0 8.1 - - + -
205C ARG* 3.7 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA 3.3 10.8 - - - +
122A ALA 4.9 0.2 - - - +
123A GLU* 3.9 37.0 - - + +
126A LEU* 4.0 23.6 - - + -
127A ALA* 4.4 4.0 - - - -
130A LEU* 3.8 13.9 - - + -
134A GLY 3.7 0.4 + - - -
135A ILE* 1.3 73.2 - - - +
137A LEU* 1.3 69.7 + - - +
138A ILE* 3.3 18.2 - - + -
174A PHE* 5.6 0.7 - - + -
177A LEU* 6.3 0.7 - - + -
179A TYR* 4.1 22.9 - - + -
243A PHE 3.1 3.8 - - - +
244A ALA 3.5 0.2 - - - -
245A LEU* 2.6 75.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.3 6.5 - - + -
32A LEU* 3.9 20.6 - - + -
40A ILE* 5.7 0.7 - - + -
50A MSE 4.4 4.5 - - + -
54A TRP* 3.7 36.1 - - + -
106A VAL* 4.1 9.6 - - + -
107A ALA 3.0 7.2 + - - +
108A ALA* 3.4 26.1 - - + -
109A CYS 3.3 20.2 + - - -
110A VAL* 4.7 2.9 - - + -
126A LEU* 5.1 0.3 - - - +
135A ILE* 3.6 26.2 + - + -
136A MSE 1.3 74.8 - - - +
138A ILE* 1.3 67.5 + - - +
139A GLY 4.3 0.4 - - - -
242A VAL* 3.9 15.9 - - + -
243A PHE 3.6 1.8 - - - -
244A ALA* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A CYS* 4.0 7.0 - - + +
113A THR* 5.2 4.5 - - - +
119A PHE* 4.4 21.3 - - + +
122A ALA* 4.9 11.2 - - + -
123A GLU* 5.0 1.6 - - + +
126A LEU* 5.6 3.1 - - + -
136A MSE 3.3 35.0 - - + -
137A LEU* 1.3 84.0 - - - +
139A GLY* 1.3 61.4 + - - +
140A GLU* 3.5 15.0 + - + -
174A PHE* 3.8 28.0 - - + -
241A GLY 3.4 2.8 - - - +
242A VAL* 3.2 5.5 - - - +
243A PHE* 2.9 39.4 + - - +
245A LEU* 3.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A CYS 3.4 9.3 + - - -
110A VAL* 3.8 12.9 - - - +
111A GLY* 3.2 31.5 + - - -
113A THR* 4.0 14.4 - - - +
138A ILE* 1.3 71.8 - - - +
140A GLU* 1.3 59.5 + - - +
141A PRO* 4.5 0.2 - - - +
240A TRP* 3.9 12.4 + - - -
241A GLY 3.2 10.8 - - - -
242A VAL* 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 3.1 21.4 - - + +
118A GLY* 3.5 5.8 - - - +
119A PHE* 3.3 33.3 - - + +
138A ILE* 3.5 17.5 + - + +
139A GLY* 1.3 74.1 - - - +
141A PRO* 1.3 96.4 - - - +
142A TYR* 4.0 6.4 - - - -
163A ASP 5.4 1.7 - - - +
164A PHE* 4.8 10.1 - - - -
165A LEU* 5.8 2.4 - - - +
170A LEU* 4.1 29.5 - - + +
174A PHE* 5.0 1.3 - - + -
240A TRP* 3.9 4.2 - - - +
241A GLY 3.1 22.5 + - - +
243A PHE* 4.4 1.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 5.7 1.3 - - - +
113A THR* 4.8 4.5 - - + -
139A GLY 4.5 1.3 - - - +
140A GLU* 1.3 111.0 - - - +
142A TYR* 1.3 61.7 + - - +
164A PHE* 3.5 43.3 - - + +
165A LEU 4.9 1.0 + - - -
170A LEU* 4.5 0.7 - - - +
192A TRP* 5.4 4.0 - - + -
238A PHE* 5.0 9.4 - - + -
239A GLY 3.4 11.2 - - - +
240A TRP* 3.4 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU 4.0 5.8 - - - -
141A PRO* 1.3 77.4 - - - +
143A TRP* 1.3 61.6 + - - +
144A ARG* 3.9 16.3 - - + +
164A PHE* 4.3 5.4 - - - -
165A LEU 3.2 15.5 - - - +
166A THR 4.2 1.6 - - - -
167A LEU* 3.7 44.3 - - + +
170A LEU* 3.9 18.4 - - + -
186A LEU* 3.7 31.1 - - + +
187A ALA 4.6 4.2 + - - -
238A PHE* 3.7 7.3 - - - -
239A GLY* 2.8 48.3 + - - +
240A TRP* 3.0 35.3 + - - -
243A PHE* 4.9 0.9 - + - -
235C ARG* 5.1 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 1.3 71.7 - - - +
144A ARG* 1.3 61.3 + - - +
145A GLN 2.9 4.9 + - - -
146A LEU* 3.6 35.5 + - + +
147A PRO* 3.7 16.4 - - + -
153A ALA* 4.4 10.5 - - + -
156A CYS* 4.4 6.1 - - + -
158A VAL* 3.5 32.3 - - + -
160A SER 4.0 7.9 - - - -
161A THR* 2.8 28.3 + - - +
164A PHE* 3.2 42.1 + + + +
165A LEU 2.6 16.2 + - - +
166A THR* 3.9 18.4 + - - -
167A LEU 4.6 0.2 + - - -
237A CYS* 3.2 35.4 - - + -
238A PHE* 3.5 33.7 - + - -
----------------------------------------------------------
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