Contacts of the helix formed by residues 128 - 146 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 3.5 44.6 - - + +
125B LYS 4.4 7.9 - - - +
126B ASP* 2.8 21.7 + - - +
127B ASN* 1.3 74.2 - - - +
129B LYS* 1.3 54.8 + - - +
130B THR* 3.6 14.1 - - + -
131B ILE* 3.1 15.3 + - + +
132B ALA* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 1.3 74.9 - - - +
130B THR* 1.3 58.0 + - - +
132B ALA* 3.2 6.3 + - - +
133B GLU* 2.9 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.9 19.4 - - - +
27B GLY 4.0 5.4 - - - +
28B LYS* 3.2 32.8 - - - +
29B ASP 5.3 0.7 - - - -
30B GLY* 4.6 13.9 - - - -
65B ALA* 4.7 2.9 - - + -
66B MET* 3.8 8.3 - - - +
128B VAL* 3.6 8.5 - - + -
129B LYS* 1.3 78.3 - - - +
131B ILE* 1.3 71.6 + - + +
133B GLU* 4.2 5.7 - - - +
134B GLN* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 4.0 21.3 - - + +
66B MET* 3.5 23.8 - - + -
115B TYR* 4.1 19.9 - - + -
120B ILE* 4.7 18.4 - - + -
126B ASP 4.3 7.2 - - - +
127B ASN* 3.3 20.6 - - - +
128B VAL* 3.1 27.3 + - + +
130B THR* 1.3 76.8 - - + +
132B ALA* 1.3 65.1 + - - +
134B GLN* 3.1 2.6 + - - +
135B ARG* 3.0 37.5 + - - +
395B VAL* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 3.4 29.1 + - - +
128B VAL 2.8 20.5 + - - +
129B LYS* 3.7 6.3 - - - +
131B ILE* 1.3 73.8 - - - +
133B GLU* 1.3 60.7 + - + +
135B ARG* 3.4 12.4 - - - +
136B THR* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LYS* 2.9 54.5 + - + +
130B THR* 4.2 5.3 - - - +
132B ALA* 1.3 76.8 - - + +
134B GLN* 1.3 66.2 + - - +
136B THR* 3.7 6.3 + - - -
137B LYS* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 3.8 25.3 - - + -
113B VAL* 3.3 34.0 - - + +
115B TYR* 3.5 18.4 - - + +
130B THR 3.3 16.0 + - - +
131B ILE 3.1 4.4 + - - +
133B GLU* 1.3 75.8 - - - +
135B ARG* 1.3 59.0 + - - +
136B THR 3.1 1.3 - - - -
137B LYS* 2.8 40.8 + - - +
138B GLU* 2.8 18.5 + - - +
141B GLU* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 3.0 19.5 + - + +
120B ILE* 2.8 31.7 + - - +
121B LEU 3.7 3.0 + - - -
122B PRO* 3.5 15.4 - - - +
127B ASN* 3.0 37.6 + - - +
131B ILE* 3.0 19.2 + - - +
132B ALA* 3.4 14.8 - - - +
134B GLN* 1.3 77.2 - - - +
136B THR* 1.3 65.8 + - - +
138B GLU* 3.9 1.9 - - - +
139B VAL* 3.3 30.1 + - - +
393B PRO* 3.7 15.6 - - + +
395B VAL* 3.6 21.0 - - + +
396B HIS* 4.5 3.6 - - - -
507B GLU* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA 3.0 18.2 + - - -
133B GLU* 3.7 7.4 + - - -
134B GLN 3.1 0.6 - - - -
135B ARG* 1.3 80.0 - - - +
137B LYS* 1.3 61.1 + - - +
139B VAL* 3.9 3.9 + - - +
140B SER* 3.2 24.8 + - - -
507B GLU* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN* 5.7 6.3 - - - +
133B GLU 3.5 10.4 + - - +
134B GLN* 2.8 28.6 + - - +
136B THR* 1.3 79.7 - - - +
138B GLU* 1.3 58.7 + - - +
140B SER* 3.1 6.4 + - - -
141B GLU* 2.8 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 4.5 8.3 + - - -
113B VAL* 4.5 15.9 - - + +
115B TYR* 3.1 18.2 + - - +
134B GLN* 2.8 20.8 + - - +
135B ARG 3.9 2.5 - - - +
137B LYS* 1.3 75.8 - - - +
139B VAL* 1.3 63.1 + - - +
141B GLU* 3.2 15.6 + - - +
142B ASN* 3.0 40.4 + - - +
393B PRO* 3.1 28.9 - - + +
394B SER* 2.7 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG 3.3 18.2 + - - +
136B THR* 4.2 4.0 - - - +
138B GLU* 1.3 79.8 - - - +
140B SER* 1.3 62.4 + - - +
142B ASN* 3.4 8.6 + - - +
143B LYS* 3.1 35.4 + - - +
389B TRP 4.9 0.7 - - - -
390B ARG 3.1 26.2 - - - +
391B ASN* 3.9 9.6 - - - +
392B LEU 3.7 8.5 - - - +
393B PRO* 3.6 35.0 - - + -
507B GLU* 5.3 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 3.2 21.0 + - - -
137B LYS* 3.1 9.3 + - - -
139B VAL* 1.3 79.8 - - - +
141B GLU* 1.3 62.1 + - - +
143B LYS* 3.6 15.6 + - - +
144B LYS* 3.7 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 5.6 4.9 - - - +
134B GLN* 5.4 1.6 - - - +
137B LYS* 2.8 57.1 + - + +
138B GLU* 3.5 14.4 - - - +
140B SER* 1.3 77.9 - - - +
142B ASN* 1.3 64.1 + - - +
144B LYS* 3.1 29.8 + - + +
145B LEU* 3.8 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 5.5 2.5 + - - +
138B GLU* 3.0 37.9 + - - +
139B VAL* 3.8 4.5 - - - +
140B SER 3.3 0.4 - - - -
141B GLU* 1.3 74.7 - - - +
143B LYS* 1.3 61.3 + - - +
144B LYS 3.0 5.6 - - - -
145B LEU* 2.9 22.1 + - - +
146B TYR* 3.0 25.3 + - + +
389B TRP* 3.0 56.1 + - - +
392B LEU 4.8 6.5 + - - -
399B TRP* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.1 29.3 + - - +
140B SER* 3.8 11.5 - - - +
141B GLU 3.3 0.6 - - - -
142B ASN* 1.3 75.4 - - - +
144B LYS* 1.3 60.7 + - + +
145B LEU 3.3 0.2 - - - -
146B TYR 3.8 3.0 - - - +
147B LYS* 3.1 34.5 - - - +
390B ARG* 2.7 68.8 + - + +
391B ASN* 4.0 14.5 + - - +
510B ASP* 5.9 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.7 24.9 + - - +
141B GLU* 3.4 14.4 - - + +
142B ASN 3.0 0.8 - - - -
143B LYS* 1.3 78.0 - - + +
145B LEU* 1.3 65.4 + - + +
146B TYR 3.6 0.2 - - - -
147B LYS* 4.2 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 4.1 12.3 - - + +
142B ASN* 2.9 15.5 + - - +
144B LYS* 1.3 85.3 - - + +
146B TYR* 1.3 80.8 + - + +
147B LYS* 3.8 4.0 + - - +
162B VAL* 5.3 1.4 - - - +
163B ASP 5.1 5.9 - - - +
171B PRO* 4.2 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASN* 3.0 24.9 + - - +
143B LYS 3.8 2.2 - - - +
145B LEU* 1.3 92.9 - - + +
147B LYS* 1.3 62.9 + - - +
162B VAL* 4.4 9.2 - - + -
171B PRO* 3.3 36.0 - - + +
173B ASP* 4.5 3.1 + - - +
174B VAL* 3.6 29.9 - - + +
386B VAL* 4.7 7.9 - - + +
389B TRP* 3.3 63.7 - + + -
390B ARG* 3.1 34.5 + - + +
410B MET* 4.1 16.8 - - + -
----------------------------------------------------------
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