Contacts of the strand formed by residues 138 - 148 (chain B) in PDB entry 1V8C
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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.2 11.7 - - + -
21A PRO* 4.9 1.6 - - + -
31A ASN* 3.7 40.2 - - + +
34A ARG* 4.0 23.8 - - + +
35A ALA* 3.7 14.3 - - - +
134B LYS* 3.3 5.7 - - - +
135B VAL 2.9 40.2 + - - +
136B GLY 3.3 0.2 - - - -
137B SER* 1.3 78.6 - - - +
139B SER* 1.3 78.7 + - - +
140B ILE* 3.8 18.4 + - + +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 3.5 25.5 - - - +
133B LEU 3.5 6.2 + - - -
134B LYS* 4.2 10.5 - - - -
137B SER 3.9 3.2 + - - -
138B LEU* 1.3 86.8 - - - +
140B ILE* 1.3 61.0 + - - +
141B PRO* 3.4 11.7 - - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 4.3 4.7 - - - +
20A LEU* 4.7 0.4 - - + -
21A PRO* 3.7 37.9 - - + -
94B GLY* 4.3 2.7 - - - -
95B ALA* 4.2 6.3 - - + +
132B PRO* 3.3 3.7 - - - +
133B LEU* 2.8 48.1 + - + +
135B VAL* 3.6 32.5 - - + -
138B LEU* 4.0 21.8 - - + +
139B SER* 1.3 75.0 - - - +
141B PRO* 1.3 76.7 - - + +
142B GLN* 3.6 13.2 + - - +
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ALA* 2.9 42.3 + - + +
96B PHE 5.5 1.1 - - - +
129B GLU* 4.1 17.0 - - - +
132B PRO* 4.2 8.7 - - + -
139B SER* 3.4 11.0 - - - +
140B ILE* 1.3 85.3 - - + +
142B GLN* 1.3 68.9 + - - +
143B LEU 4.2 0.7 - - - -
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.5 20.5 - - + +
93B PHE 3.5 1.8 - - - -
94B GLY* 3.5 16.2 - - - -
129B GLU* 3.2 9.2 + - - +
130B VAL* 2.8 54.0 + - + +
131B GLU 3.2 18.8 - - - +
132B PRO* 4.4 0.4 - - - +
133B LEU* 3.4 40.3 - - + +
140B ILE* 3.6 14.2 + - - +
141B PRO* 1.3 88.8 + - - +
143B LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG 3.6 0.2 - - - +
92B THR* 3.2 2.0 - - - -
93B PHE* 2.6 47.7 + - + +
96B PHE* 3.2 37.9 - - + +
97B PRO 4.6 0.2 - - - -
98B PRO* 4.0 27.4 - - + -
101B LEU* 3.9 27.8 - - + -
127B PHE* 4.3 7.4 - - + -
128B ARG* 3.6 32.3 - - - +
129B GLU* 3.9 9.4 - - - +
141B PRO 4.2 0.6 - - - -
142B GLN* 1.3 71.5 - - - +
144B ARG* 1.3 59.9 + - - +
145B VAL* 3.6 9.6 + - + -
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 2.9 42.7 + - - +
91B ARG 3.7 4.7 - - - +
92B THR* 4.0 17.2 - - - +
126B ARG 3.8 0.5 - - - +
127B PHE* 3.1 5.2 - - - +
128B ARG* 2.9 38.0 + - + +
130B VAL* 3.9 21.0 - - + +
142B GLN 3.9 2.0 + - - -
143B LEU* 1.3 70.5 - - - +
145B VAL* 1.3 61.0 + - - +
146B GLU* 3.1 32.7 + - + +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE 3.9 0.2 - - - +
90B GLU* 3.1 25.1 - - - +
91B ARG 2.9 16.9 + - - +
93B PHE* 3.6 29.4 - - + -
96B PHE* 5.0 0.2 - - + -
101B LEU* 4.1 12.1 - - + -
125B VAL* 3.9 25.8 - - + -
126B ARG 3.5 3.6 - - - +
127B PHE* 4.0 12.1 - - + -
143B LEU* 4.0 12.1 - - + +
144B ARG* 1.3 78.3 - - - +
146B GLU* 1.3 63.6 + - - +
147B VAL* 4.2 11.8 + - + -
156B PHE* 4.6 3.9 - - + -
159B ILE* 4.2 14.4 - - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE 3.5 4.9 - - - +
90B GLU* 3.9 17.0 - - + +
124B VAL 3.7 1.0 - - - +
125B VAL* 3.5 1.2 - - - +
126B ARG* 2.6 65.6 + - + +
127B PHE* 5.8 0.2 - - - -
144B ARG* 3.1 41.1 + - + +
145B VAL* 1.3 75.7 - - - +
147B VAL* 1.3 66.2 + - - +
148B GLU* 5.4 9.0 - - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 3.4 4.7 - - - -
89B PHE 2.9 33.6 + - - +
123B ALA* 4.1 13.0 - - + -
124B VAL 3.5 5.4 - - - +
125B VAL* 4.4 6.1 - - + -
145B VAL* 4.2 6.3 - - + -
146B GLU* 1.3 80.3 - - - +
148B GLU* 1.3 66.1 + - - +
152B ALA* 3.6 33.7 - - + +
155B TRP* 4.2 4.9 - - + -
156B PHE* 4.0 37.0 - - + +
159B ILE* 4.1 18.8 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 4.3 15.6 - - - +
123B ALA* 3.0 4.7 - - - +
124B VAL* 2.7 51.2 + - + +
126B ARG* 5.2 13.3 + - - -
146B GLU* 5.4 7.9 - - + +
147B VAL* 1.3 81.6 - - - +
149B GLY* 1.3 57.8 + - - +
152B ALA* 3.7 8.1 - - - -
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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