Contacts of the helix formed by residues 116 - 130 (chain A) in PDB entry 2VZE
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TRP* 4.6 7.4 - - + -
113A LEU* 4.5 8.7 - - + -
114A PRO* 2.8 38.0 + - + +
115A ARG* 1.3 76.6 - - - +
117A PRO* 1.3 78.0 - - + +
118A GLU* 3.1 24.5 - - + +
119A TRP* 3.0 15.3 + - - +
120A TRP* 3.2 14.7 - - - -
183A VAL* 4.8 4.9 - - + -
287A LEU* 3.8 19.3 - - + -
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.4 9.1 - - + +
71A TRP* 3.7 43.0 - - + +
79A LEU* 4.6 4.5 - - + -
81A TRP* 3.4 40.2 - - + -
116A VAL* 1.3 88.5 - - + +
118A GLU* 1.3 71.1 + - - +
120A TRP* 2.9 23.3 + - + +
121A LEU* 3.1 15.4 + - + +
285A VAL* 6.5 0.2 - - + -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.2 1.6 - - + -
116A VAL* 3.1 22.5 + - + +
117A PRO* 1.3 83.8 - - - +
119A TRP* 1.3 57.1 + - - +
121A LEU* 3.8 15.2 - - + +
122A VAL* 2.8 36.8 + - - +
183A VAL* 3.4 40.1 - - + +
194A PHE* 3.8 21.8 - - + -
195A LYS* 2.9 33.2 + - + +
198A LEU* 5.3 3.6 - - + +
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Residues in contact with TRP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.6 27.8 + - + +
113A LEU* 3.8 21.4 - - + +
114A PRO 4.3 7.0 - - - +
116A VAL* 3.0 14.6 + - - +
118A GLU* 1.3 78.7 - - - +
120A TRP* 1.3 81.6 + + + +
122A VAL* 3.9 1.3 - - - +
123A ILE* 3.0 57.6 + - + +
133A PHE* 5.7 0.2 - + - -
135A PRO* 4.1 16.3 - - + +
219A TYR* 4.8 2.0 - - - -
263A THR* 3.2 47.3 + - + -
268A ASN* 3.1 34.5 - - + -
269A ILE* 4.2 18.2 - - + -
273A LEU* 4.2 17.5 - - + -
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Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.2 18.8 - - + -
86A LEU* 5.5 0.7 - - + -
115A ARG* 4.3 8.7 - - + -
116A VAL 3.2 36.1 - - - -
117A PRO* 2.9 10.5 + - + +
119A TRP* 1.3 98.6 - + + +
121A LEU* 1.3 57.5 + - - +
123A ILE* 3.6 1.6 + - - +
124A LEU* 3.1 37.4 + - - +
259A THR 6.1 0.2 - - - -
263A THR* 4.6 3.6 - - + -
268A ASN* 3.6 21.8 - - - -
272A SER* 3.2 37.6 + - - -
273A LEU* 3.9 25.8 - - + +
277A TRP* 3.9 20.9 - + + -
283A THR* 4.6 0.6 - - - +
285A VAL* 3.5 43.8 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 5.6 1.6 - - + -
81A TRP* 4.3 15.9 - - + +
86A LEU* 4.3 21.8 - - + -
89A ASN* 3.6 42.2 - - + +
90A SER* 4.0 14.7 - - - +
93A ALA* 3.3 20.3 - - + +
117A PRO* 3.1 16.4 + - + +
118A GLU* 3.7 18.6 - - + +
120A TRP* 1.3 78.1 - - + +
122A VAL* 1.3 56.1 + - - +
124A LEU* 3.6 5.3 + - - +
125A GLY 2.9 22.9 + - - -
194A PHE* 5.1 4.0 - - + -
198A LEU* 4.3 15.3 - - + -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA* 4.7 4.3 - - - -
97A LEU* 4.0 8.9 - - + +
111A VAL* 3.7 29.2 - - + -
113A LEU* 4.6 3.4 - - + -
118A GLU* 2.8 30.4 + - + +
119A TRP* 3.9 4.9 - - - +
121A LEU* 1.3 71.2 - - - +
123A ILE* 1.3 61.5 + - + +
125A GLY* 3.1 1.4 + - - -
126A CYS* 2.9 35.8 + - - -
158A VAL* 4.1 28.3 - - + -
194A PHE* 3.8 31.9 - - + -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.0 22.4 - - + -
119A TRP* 3.0 53.9 + - + +
120A TRP 4.0 2.9 - - - +
122A VAL* 1.3 75.0 - - - +
124A LEU* 1.3 65.1 + - - +
126A CYS* 3.2 7.0 + - - +
127A ILE* 3.0 33.6 + - + +
133A PHE* 3.8 38.1 - - + -
135A PRO* 4.6 1.1 - - + -
269A ILE* 3.4 30.7 - - + -
273A LEU* 4.0 7.2 - - + -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.9 7.0 - - + -
47A ALA* 4.7 10.7 - - + +
51A LEU* 3.5 34.1 - - + -
86A LEU* 4.0 16.4 - - + -
90A SER* 3.9 16.8 - - - -
120A TRP 3.1 22.1 + - - +
121A LEU* 3.8 4.5 - - - +
123A ILE* 1.3 75.4 - - - +
125A GLY* 1.3 58.0 + - - +
127A ILE* 3.3 15.6 + - + +
128A ARG* 3.0 36.2 + - - +
273A LEU* 4.5 13.9 - - + -
277A TRP* 3.5 28.7 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER 3.9 5.4 + - - -
94A ALA* 3.7 27.8 - - - +
97A LEU* 3.7 10.1 - - - -
121A LEU 2.9 16.1 + - - -
122A VAL 3.1 5.3 + - - -
124A LEU* 1.3 77.4 - - - +
126A CYS* 1.3 61.0 + - - +
128A ARG 3.5 0.3 + - - -
129A ALA* 3.0 27.4 + - - +
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.3 10.8 - - - -
109A VAL* 4.2 17.7 - - - -
122A VAL* 2.9 26.4 + - - -
123A ILE 3.5 7.2 - - - +
125A GLY* 1.3 73.9 - - - +
127A ILE* 1.3 64.6 + - - +
129A ALA 3.1 0.5 + - - -
130A GLY 2.9 5.4 + - - -
131A LEU* 2.7 61.4 + - + +
133A PHE* 4.1 24.9 - - + -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 2.9 43.9 + - - +
46A PHE* 4.2 10.5 - - + +
47A ALA* 3.9 13.9 - - + +
123A ILE* 3.0 32.5 + - + +
124A LEU* 3.3 19.0 + - + +
126A CYS* 1.3 74.7 - - - +
128A ARG* 1.3 62.9 + - - +
130A GLY* 3.5 5.7 + - - -
131A LEU 4.9 0.7 - - - -
133A PHE* 3.7 22.0 - - + -
210A THR* 4.3 0.2 - - - +
216A SER* 4.3 5.4 - - - +
235A TYR* 3.8 18.2 + - + -
269A ILE* 4.8 2.0 - - + -
273A LEU* 5.6 1.3 - - + -
274A MET* 4.6 19.1 - - + -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 3.6 20.2 - - + +
51A LEU* 3.6 18.6 - - - +
52A ASP* 2.9 41.2 + - - -
87A SER* 3.7 5.9 + - - -
90A SER* 3.1 49.0 + - - -
91A GLN* 3.4 27.5 - - - +
94A ALA* 3.9 3.1 - - + -
124A LEU* 3.0 19.0 + - - +
125A GLY 3.8 4.3 - - - +
127A ILE* 1.3 77.3 - - - +
129A ALA* 1.3 57.9 + - - +
130A GLY 3.2 2.8 + - - -
205A HIS* 3.5 21.6 + - + +
207A CYS* 3.8 18.4 - - - +
208A VAL* 2.9 30.5 + - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 4.3 5.6 - - + +
98A SER* 4.0 25.0 - - - +
103A LEU 5.4 0.2 - - - +
105A ARG* 4.0 9.4 + - - +
125A GLY 3.0 18.3 + - - +
128A ARG* 1.3 75.3 - - - +
130A GLY* 1.3 62.0 - - - +
131A LEU* 3.5 28.2 + - + +
205A HIS* 4.0 11.4 - - - +
208A VAL* 3.8 14.1 - - - +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.5 11.3 - - - +
106A GLY* 3.0 25.3 + - - -
126A CYS 2.9 2.6 + - - -
127A ILE 3.5 3.1 + - - -
128A ARG 3.2 5.7 + - - -
129A ALA* 1.3 79.1 - - - +
131A LEU* 1.3 61.0 + - - +
132A ILE* 5.2 1.0 - - - +
208A VAL* 4.5 1.3 - - - -
210A THR* 4.0 13.0 - - - -
214A GLU* 4.8 2.1 - - - +
215A ALA 5.3 1.0 - - - +
235A TYR* 3.2 21.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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