Contacts of the helix formed by residues 128 - 146 (chain A) in PDB entry 3VF1
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 VAL 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 3.5 43.7 - - + +
125A LYS 4.4 7.4 - - - +
126A ASP* 2.8 22.2 + - - +
127A ASN* 1.3 73.4 - - - +
129A LYS* 1.3 55.2 + - - +
130A THR* 3.6 13.7 - - + -
131A ILE* 3.1 15.2 + - + +
132A ALA* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 1.3 74.7 - - - +
130A THR* 1.3 59.2 + - - +
132A ALA* 3.2 6.5 + - - +
133A GLU* 2.9 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.9 18.9 - - - +
27A GLY 4.0 4.7 - - - +
28A LYS* 3.2 32.8 - - - +
29A ASP 5.4 0.2 - - - -
30A GLY* 4.6 13.4 - - - -
65A ALA* 4.7 3.1 - - + -
66A MET* 3.8 9.2 - - - +
128A VAL* 3.6 9.2 - - + -
129A LYS* 1.3 79.4 - - - +
131A ILE* 1.3 72.1 + - + +
133A GLU* 4.2 6.6 - - - +
134A GLN* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 4.0 21.5 - - + +
66A MET* 3.5 24.9 - - + -
115A TYR* 4.1 19.9 - - + -
120A ILE* 4.7 18.4 - - + -
126A ASP 4.3 6.7 - - - +
127A ASN* 3.3 19.7 - - - +
128A VAL* 3.1 27.0 + - + +
130A THR* 1.3 76.4 - - + +
132A ALA* 1.3 65.7 + - - +
134A GLN* 3.1 2.6 + - - +
135A ARG* 3.0 38.1 + - - +
395A VAL* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 3.4 29.1 + - - +
128A VAL 2.8 20.9 + - - +
129A LYS* 3.7 6.5 - - - +
131A ILE* 1.3 73.8 - - - +
133A GLU* 1.3 60.0 + - + +
135A ARG* 3.4 12.0 - - - +
136A THR* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 2.9 54.1 + - + +
130A THR* 4.2 5.8 - - - +
132A ALA* 1.3 76.8 - - + +
134A GLN* 1.3 65.1 + - - +
136A THR* 3.7 6.0 + - - -
137A LYS* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.8 25.6 - - + -
113A VAL* 3.3 34.1 - - + +
115A TYR* 3.5 17.7 - - + +
130A THR 3.3 17.4 + - - +
131A ILE 3.1 4.1 + - - +
133A GLU* 1.3 76.4 - - - +
135A ARG* 1.3 59.2 + - - +
136A THR 3.1 2.0 - - - -
137A LYS* 2.8 42.6 + - - +
138A GLU* 2.8 18.2 + - - +
141A GLU* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 3.0 19.9 + - + +
120A ILE* 2.8 31.1 + - - +
121A LEU 3.7 3.0 + - - -
122A PRO* 3.5 15.8 - - - +
127A ASN* 3.0 38.5 + - - +
131A ILE* 3.0 18.9 + - - +
132A ALA* 3.4 14.1 - - - +
134A GLN* 1.3 77.0 - - - +
136A THR* 1.3 65.0 + - - +
138A GLU* 3.9 1.4 - - - +
139A VAL* 3.3 30.1 + - - +
393A PRO* 3.7 15.1 - - + +
395A VAL* 3.6 22.0 - - + +
396A HIS* 4.5 3.8 - - - +
507A GLU* 2.8 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA 3.0 18.8 + - - -
133A GLU* 3.7 7.5 + - - -
134A GLN 3.1 0.8 - - - -
135A ARG* 1.3 80.8 - - - +
137A LYS* 1.3 62.4 + - - +
139A VAL* 3.9 3.9 + - - +
140A SER* 3.2 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 5.7 6.5 - - - +
133A GLU 3.5 9.5 + - - +
134A GLN* 2.8 29.0 + - - +
136A THR* 1.3 78.7 - - - +
138A GLU* 1.3 59.6 + - - +
140A SER* 3.1 6.6 + - - -
141A GLU* 2.8 66.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
106A ARG* 4.5 8.3 + - - -
113A VAL* 4.5 16.1 - - + +
115A TYR* 3.1 18.6 + - + +
134A GLN* 2.8 21.8 + - - +
135A ARG 3.9 2.7 - - - +
137A LYS* 1.3 76.2 - - - +
139A VAL* 1.3 63.4 + - - +
141A GLU* 3.1 14.7 + - - +
142A ASN* 3.0 39.8 + - - +
393A PRO* 3.1 28.5 - - - +
394A SER* 2.7 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG 3.3 18.1 + - - +
136A THR* 4.2 3.8 - - - +
138A GLU* 1.3 79.2 - - - +
140A SER* 1.3 63.4 + - - +
142A ASN* 3.4 8.3 + - - +
143A LYS* 3.1 35.5 + - - +
389A TRP 4.9 0.4 - - - -
390A ARG 3.1 26.6 - - - +
391A ASN* 4.0 9.0 - - - +
392A LEU 3.7 8.7 - - - +
393A PRO* 3.6 34.1 - - + -
507A GLU* 5.3 2.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
136A THR* 3.2 21.8 + - - -
137A LYS* 3.1 9.5 + - - -
139A VAL* 1.3 80.6 - - - +
141A GLU* 1.3 61.6 + - - +
143A LYS* 3.6 15.7 + - - +
144A LYS* 3.7 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 5.6 4.7 - - - +
134A GLN* 5.4 1.0 - - - +
137A LYS* 2.8 57.5 + - + +
138A GLU* 3.5 14.4 - - - +
140A SER* 1.3 77.5 - - - +
142A ASN* 1.3 65.8 + - - +
144A LYS* 3.1 29.6 + - + +
145A LEU* 3.8 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 5.5 3.2 + - - +
138A GLU* 3.0 37.9 + - - +
139A VAL* 3.8 4.9 - - - +
140A SER 3.3 0.4 - - - -
141A GLU* 1.3 75.1 - - - +
143A LYS* 1.3 62.3 + - - +
144A LYS 3.0 5.2 - - - -
145A LEU* 2.9 21.7 + - - +
146A TYR* 3.0 25.5 + - + +
389A TRP* 3.0 55.7 + - - +
392A LEU 4.8 6.3 + - - -
399A TRP* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.1 27.9 + - - +
140A SER* 3.8 10.7 - - - +
141A GLU 3.3 0.4 - - - -
142A ASN* 1.3 75.3 - - - +
144A LYS* 1.3 59.4 + - + +
146A TYR 3.8 3.0 - - - +
147A LYS* 3.1 35.3 + - - +
389A TRP 4.5 0.2 + - - -
390A ARG* 2.7 70.0 + - + +
391A ASN* 4.0 13.2 + - - +
510A ASP* 5.9 1.8 + - - +
514A ASP* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.7 24.2 - - - +
141A GLU* 3.3 14.2 - - + +
142A ASN 3.0 0.6 - - - -
143A LYS* 1.3 79.9 - - + +
145A LEU* 1.3 66.4 + - + +
147A LYS* 4.2 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 4.1 12.8 - - + +
142A ASN* 2.9 14.8 + - - +
144A LYS* 1.3 86.6 - - + +
146A TYR* 1.3 83.5 + - + +
147A LYS* 3.8 3.6 + - - +
162A VAL* 5.3 0.9 - - - +
163A ASP 5.1 6.1 - - - +
171A PRO* 4.2 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.0 25.3 + - - +
143A LYS 3.8 2.6 - - - +
145A LEU* 1.3 94.0 - - + +
147A LYS* 1.3 60.5 + - - +
162A VAL* 4.4 9.4 - - + -
171A PRO* 3.3 35.1 - - + +
173A ASP* 4.5 3.5 - - - +
174A VAL* 3.6 29.8 - - + +
386A VAL* 4.7 8.1 - - + +
389A TRP* 3.3 64.4 - + + -
390A ARG* 3.1 34.2 + - + +
410A MET* 4.1 17.7 - - + -
----------------------------------------------------------
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