Contacts of the strand formed by residues 134 - 146 (chain A) in PDB entry 3ZVU
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 ARG 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A HIS* 5.6 8.3 + - - -
130A GLU* 3.4 2.7 - - - +
131A LYS* 2.6 79.2 + - - +
132A GLU* 3.7 16.0 + - + +
133A ASN* 1.3 74.5 - - - +
135A ILE* 1.3 63.5 + - - +
136A TRP* 3.2 39.9 - - + -
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Residues in contact with ILE 135 (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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39A HIS* 5.1 2.3 - - - -
40A ALA* 4.4 11.1 + - - +
41A PRO* 4.6 8.7 - - + -
42A PRO* 3.9 27.8 - - + -
128A ARG* 3.9 15.7 - - - +
129A PHE 3.4 10.5 - - - +
130A GLU* 3.8 28.9 - - + +
133A ASN 5.0 5.8 - - - +
134A ARG* 1.3 77.9 - - - +
136A TRP* 1.3 64.5 + - - +
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Residues in contact with TRP 136 (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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9A GLU* 3.7 20.4 + - + -
37A ARG* 4.3 15.9 - - + +
38A ILE 3.9 11.4 - - - +
39A HIS* 4.2 19.5 - + + +
40A ALA 4.0 4.0 - - - +
129A PHE* 2.7 86.1 + + + +
130A GLU 3.7 3.8 - - - -
131A LYS* 3.1 40.4 - - + -
134A ARG* 3.2 67.8 - - + -
135A ILE* 1.3 75.4 - - - +
137A THR* 1.3 61.8 + - - +
138A VAL* 4.5 1.8 - - + -
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Residues in contact with THR 137 (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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36A GLN 3.8 0.5 - - - +
37A ARG 3.9 0.2 - - - -
38A ILE* 3.0 39.0 + - - +
40A ALA 3.4 7.1 + - - -
42A PRO* 2.8 42.7 - - + +
45A VAL* 4.5 11.2 - - + -
126A VAL* 3.3 33.2 - - + -
127A HIS 2.7 22.8 + - - +
136A TRP* 1.3 73.4 + - - +
138A VAL* 1.3 66.0 + - - +
139A VAL 4.0 0.4 + - - +
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Residues in contact with VAL 138 (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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5A LEU* 4.2 11.9 - - + -
9A GLU* 3.7 25.1 - - + +
13A LEU* 3.9 20.0 - - + -
35A ALA* 4.5 0.4 - - + -
36A GLN 3.5 9.2 - - - +
37A ARG* 4.5 13.9 - - + -
127A HIS* 2.8 41.4 + - + -
129A PHE* 3.7 29.1 - - + -
136A TRP* 4.5 1.3 - - + -
137A THR* 1.3 77.3 - - - +
139A VAL* 1.3 72.5 + - - +
140A LEU* 4.1 10.1 - - + -
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Residues in contact with VAL 139 (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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34A HIS 3.9 0.3 - - - +
35A ALA* 3.3 4.2 - - - -
36A GLN* 2.8 38.9 + - + +
38A ILE* 3.8 13.0 - - + -
45A VAL* 3.5 32.3 - - + -
49A VAL* 5.2 0.2 - - + -
124A THR* 3.7 23.8 - - + -
125A THR 3.4 4.5 - - - +
126A VAL* 4.3 9.9 - - + -
137A THR* 4.9 0.9 - - + -
138A VAL* 1.3 79.4 - - - +
140A LEU* 1.3 63.6 + - - +
168A LEU* 3.5 30.4 - - + +
171A LEU* 4.0 6.5 - - + -
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Residues in contact with LEU 140 (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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2A ALA* 5.9 0.4 - - + -
5A LEU* 4.7 5.6 - - + -
13A LEU* 4.3 18.4 - - + +
16A SER* 4.8 0.9 - - - -
17A ILE* 3.7 30.3 - - + -
21A HIS* 3.6 16.5 - - + +
33A LEU* 4.4 7.9 - - + -
34A HIS 3.3 4.5 - - - +
35A ALA* 3.7 27.6 - - + -
124A THR* 3.3 4.7 - - - +
125A THR* 2.8 41.8 + - - +
127A HIS* 3.5 28.9 - - + +
138A VAL* 4.1 9.2 - - + -
139A VAL* 1.3 75.7 - - - +
141A GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 141 (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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33A LEU* 3.5 1.5 - - - -
34A HIS* 2.7 46.7 + - - +
58A TYR* 4.8 11.4 + - - -
59A LYS* 5.9 1.8 - - - -
108A PHE* 5.4 1.9 - - - -
120A TYR* 4.5 1.9 + - - -
122A SER* 4.2 11.9 + - - +
123A VAL 3.3 6.7 - - - +
124A THR* 2.6 31.2 + - + +
139A VAL 4.3 0.2 - - - -
140A LEU* 1.3 75.4 - - - +
142A SER* 1.3 66.7 + - - +
143A TYR* 6.2 0.7 - - + -
164A VAL* 3.7 30.4 - - + +
167A ASN* 5.3 4.0 + - - +
168A LEU* 4.2 28.4 - - + +
192A A8S 4.2 11.4 - - - +
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Residues in contact with SER 142 (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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20A PHE 3.9 0.5 + - - -
21A HIS* 2.6 38.8 + - - -
23A TYR* 2.6 31.4 + - - -
32A SER 3.2 15.3 - - - -
33A LEU* 3.9 7.0 - - - -
122A SER* 3.2 6.3 - - - -
123A VAL* 3.0 29.2 + - - +
141A GLU* 1.3 77.1 - - - +
143A TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.1 5.8 - - - -
30A CYS 4.8 0.4 - - - -
31A SER* 2.5 43.1 - - - -
32A SER* 3.1 31.1 + - - -
34A HIS* 4.2 7.6 - + - -
120A TYR* 3.4 44.2 - + + +
121A LYS 3.3 9.9 - - - +
122A SER* 3.9 1.3 - - - -
141A GLU* 6.2 0.4 - - + -
142A SER* 1.3 78.2 - - - +
144A VAL* 1.3 64.2 + - - +
145A VAL* 4.0 13.7 - - + -
157A ARG* 3.3 22.6 + - + +
160A ALA* 3.4 21.9 - - + +
161A ASP* 2.5 29.5 + - - -
164A VAL* 4.1 12.8 - - + -
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Residues in contact with VAL 144 (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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23A TYR* 4.2 22.7 - - + -
25A LEU* 3.6 29.4 - - + -
29A SER* 4.1 11.9 - - - +
30A CYS 3.2 6.5 - - - +
31A SER* 3.9 3.8 - - - -
119A ASN 3.4 4.7 - - - +
120A TYR* 3.4 3.3 - - - -
121A LYS* 3.1 50.8 + - + +
143A TYR* 1.3 76.7 - - - +
145A VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 145 (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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29A SER* 3.2 3.4 - - - -
30A CYS* 2.8 40.3 + - - +
117A LEU* 4.0 23.1 - - + -
118A THR 3.5 13.2 - - - +
119A ASN 3.9 6.5 - - - -
120A TYR* 3.8 25.8 - - + -
143A TYR* 4.0 14.1 - - + -
144A VAL* 1.3 76.9 - - - +
146A ASP* 1.3 80.8 + - - +
156A THR* 3.6 26.5 - - + -
160A ALA* 5.3 2.0 - - + -
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Residues in contact with ASP 146 (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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28A GLY 3.2 12.6 - - - +
29A SER* 3.6 15.4 - - - -
116A ARG 5.4 0.2 - - - +
117A LEU* 5.3 0.3 - - - +
118A THR* 3.4 27.1 + - - +
119A ASN* 2.9 32.8 - - - +
145A VAL* 1.3 91.4 - - - +
147A MET* 1.3 68.5 + - - +
148A PRO* 3.4 8.1 - - - +
156A THR* 4.0 1.9 - - - +
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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