Contacts of the strand formed by residues 138 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU 3.6 0.5 - - - +
134A LYS* 3.5 4.7 - - - +
135A VAL* 2.9 41.3 + - + +
136A GLY 3.2 1.0 - - - -
137A SER* 1.3 79.1 - - - +
139A SER* 1.3 70.8 + - - +
140A ILE* 3.7 22.3 + - + +
20B LEU* 4.0 13.9 - - + -
21B PRO* 4.9 1.3 - - + -
31B ASN* 3.5 38.1 - - + +
34B ARG* 3.6 39.9 - - + +
35B ALA* 3.6 11.7 - - - +
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Residues in contact with SER 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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132A PRO* 3.1 26.7 - - - +
133A LEU 3.4 4.7 + - - -
134A LYS* 4.6 8.2 - - - +
137A SER 4.1 2.2 + - - -
138A LEU* 1.3 81.3 - - - +
140A ILE* 1.3 60.5 + - - +
141A PRO* 3.3 12.0 - - - +
34B ARG* 5.4 2.1 + - - -
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Residues in contact with ILE 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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94A GLY* 4.3 2.5 - - - -
95A ALA* 3.7 23.8 - - + +
132A PRO* 3.9 1.6 - - - -
133A LEU* 2.6 45.7 + - + +
135A VAL* 3.5 28.5 - - + -
138A LEU* 3.9 23.6 - - + +
139A SER* 1.3 73.8 + - - +
141A PRO* 1.3 73.4 - - + +
142A GLN* 3.1 17.9 + - - +
19B GLU* 3.9 9.2 - - + +
20B LEU* 4.5 0.7 - - + -
21B PRO* 3.8 26.0 - - + -
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Residues in contact with PRO 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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95A ALA* 2.7 41.7 + - + -
96A PHE 5.5 1.6 - - - +
97A PRO* 6.1 3.6 - - + -
129A GLU* 3.9 20.6 - - - +
132A PRO* 4.0 15.2 - - + -
139A SER* 3.3 11.9 - - - +
140A ILE* 1.3 87.7 - - + +
142A GLN* 1.3 60.8 + - - +
143A LEU 4.3 0.2 - - - -
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Residues in contact with GLN 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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92A THR* 3.8 18.2 - - + +
93A PHE 3.4 2.0 - - - -
94A GLY* 3.5 19.7 + - - -
129A GLU* 3.5 7.2 + - - +
130A VAL* 2.9 40.4 + - + +
131A GLU 3.2 25.8 - - - +
132A PRO* 4.2 3.2 - - - +
133A LEU* 3.4 37.1 - - + +
140A ILE* 3.1 21.3 + - - +
141A PRO* 1.3 90.0 + - - +
143A LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 143 (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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91A ARG 3.5 0.5 - - - +
92A THR* 3.2 3.8 - - - +
93A PHE* 2.8 40.6 + - + +
96A PHE* 3.2 35.0 - - + +
98A PRO* 3.7 29.6 - - + -
101A LEU* 3.8 33.7 - - + -
127A PHE* 4.2 5.6 - - + -
128A ARG 3.6 30.3 - - - +
129A GLU* 3.7 4.7 - - + +
142A GLN* 1.3 72.9 - - - +
144A ARG* 1.3 61.3 + - - +
145A VAL* 3.5 15.4 + - + +
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Residues in contact with ARG 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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90A GLU* 4.5 20.6 - - - +
91A ARG 3.8 4.5 - - - +
92A THR* 4.0 15.6 - - - +
126A ARG 3.9 0.5 + - - +
127A PHE* 3.1 9.4 - - - +
128A ARG* 3.0 84.3 + - - +
130A VAL* 3.9 19.1 - - + +
142A GLN 4.0 1.8 + - - -
143A LEU* 1.3 71.0 - - - +
145A VAL* 1.3 61.3 + - - +
146A GLU* 4.4 29.6 + - + +
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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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89A PHE 4.0 0.3 - - - +
90A GLU* 3.1 5.5 - - - +
91A ARG 2.8 37.8 + - - +
93A PHE* 3.8 28.3 - - + -
96A PHE* 5.2 0.2 - - + -
101A LEU* 4.0 10.5 - - + -
125A VAL* 4.0 24.2 - - + -
126A ARG 3.5 3.4 - - - +
127A PHE* 4.1 1.3 - - + -
143A LEU* 3.8 22.9 - - + +
144A ARG* 1.3 78.9 - - - +
146A GLU* 1.3 64.3 + - - +
147A VAL* 4.2 6.3 - - + -
156A PHE* 4.7 4.0 - - + -
159A ILE* 4.1 21.3 - - + -
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Residues in contact with GLU 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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89A PHE 3.4 6.3 - - - +
90A GLU* 4.1 20.8 - - + +
124A VAL 3.7 1.1 - - - +
125A VAL* 3.4 4.0 - - - +
126A ARG* 2.8 61.1 + - + +
144A ARG* 4.4 31.8 + - + +
145A VAL* 1.3 78.5 - - - +
147A VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 147 (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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88A GLY* 3.2 1.4 - - - -
89A PHE 2.9 34.4 + - - +
123A ALA* 4.0 14.8 - - + -
124A VAL 3.4 5.8 - - - +
125A VAL* 4.2 6.7 - - + -
145A VAL* 4.2 4.9 - - + -
146A GLU* 1.3 79.7 - - - +
148A GLU* 1.3 63.9 + - - +
152A ALA* 3.6 35.5 - - - +
155A TRP* 4.2 5.6 - - + -
156A PHE* 4.0 27.4 - - + +
159A ILE* 3.9 27.6 - - + -
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Residues in contact with GLU 148 (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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87A GLY 3.0 11.9 - - - +
88A GLY* 4.0 7.9 - - - -
123A ALA* 3.2 2.3 - - - -
124A VAL* 2.9 38.4 + - + +
126A ARG* 3.6 32.4 + - - +
146A GLU 4.3 0.2 - - - -
147A VAL* 1.3 76.3 - - - +
149A GLY* 1.3 59.5 + - - +
152A ALA* 3.8 4.9 - - - -
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Residues in contact with GLY 149 (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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85A ALA 4.6 0.2 - - - +
86A GLY* 4.0 4.3 - - - -
87A GLY 2.9 24.3 + - - +
122A GLY 3.5 6.7 - - - -
123A ALA* 4.3 1.3 - - - -
148A GLU* 1.3 78.8 - - - +
150A GLU* 1.3 66.2 + - - -
151A GLU 3.2 2.9 - - - -
152A ALA* 3.1 9.2 + - - +
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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