Contacts of the strand formed by residues 93 - 99 (chain A) in PDB entry 3C5C
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 ALA 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASN 3.3 2.8 + - - -
23A LEU* 3.5 18.8 - - + -
24A ALA 3.1 22.5 + - - -
91A ALA* 3.5 4.7 - - - +
92A HIS* 1.3 82.5 - - - +
94A PHE* 1.3 65.6 + - - +
127A ILE* 3.3 3.8 - - - +
128A PRO* 3.2 21.3 - - + +
130A LEU* 5.3 0.4 - - + -
179A ALA* 3.7 28.9 - - + +
182A GLU* 5.2 0.2 - - + -
183A ALA* 4.1 1.3 - - + -
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Residues in contact with PHE 94 (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 LEU* 6.3 0.2 - - - -
24A ALA* 3.3 23.6 - - + +
26A LEU* 3.9 13.7 - - + -
87A TYR* 3.6 32.5 - + - -
88A LEU* 4.2 7.4 - - + -
91A ALA* 3.7 15.5 - - + -
93A ALA* 1.3 75.1 - - - +
95A LEU* 1.3 62.4 + - - +
96A VAL* 4.6 1.6 - - + -
116A LEU* 3.6 46.0 - - + -
127A ILE* 3.5 43.7 - - + -
128A PRO 2.9 10.4 + - - -
129A ALA* 3.3 4.3 - - + -
130A LEU* 2.7 37.6 + - - +
179A ALA* 5.6 0.2 - - - -
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Residues in contact with LEU 95 (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 LEU* 5.5 3.4 - - + -
24A ALA 2.8 10.0 + - - +
25A ILE* 3.0 38.1 - - + +
26A LEU* 2.8 32.9 + - - +
36A LEU* 6.1 0.9 - - + -
94A PHE* 1.3 75.7 - - - +
96A VAL* 1.3 55.5 + - - +
97A VAL* 4.0 1.1 - - + -
130A LEU* 3.3 23.3 - - + +
132A LEU* 4.1 25.4 - - + -
175A VAL* 4.4 6.7 - - + +
176A PHE* 3.7 33.0 - - + -
179A ALA* 3.8 28.7 - - + -
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Residues in contact with VAL 96 (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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26A LEU* 3.5 14.4 - - + +
94A PHE* 4.6 2.5 - - + -
95A LEU* 1.3 74.6 - - - +
97A VAL* 1.3 57.9 + - - +
109A SER* 3.7 37.0 - - - +
112A TYR* 3.8 20.9 - - + -
113A LEU* 3.9 27.8 - - + -
116A LEU* 4.0 19.7 - - + -
129A ALA* 4.9 1.3 - - + -
130A LEU 2.8 13.0 + - - +
131A LEU* 3.4 9.4 - - + +
132A LEU 2.7 31.2 + - - -
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Residues in contact with VAL 97 (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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25A ILE* 3.6 30.3 - - + -
26A LEU 2.9 11.7 + - - +
27A GLY* 3.6 14.2 - - - -
28A ARG 4.2 1.9 + - - -
31A ALA* 3.5 25.2 - - + +
33A LYS* 4.1 10.3 - - + +
36A LEU* 3.8 31.4 - - + -
95A LEU* 4.4 2.2 - - + +
96A VAL* 1.3 76.9 - - - +
98A TYR* 1.3 71.7 + - - +
105A SER* 4.5 0.9 + - - +
109A SER* 4.5 5.3 - - - -
132A LEU* 3.4 17.9 - - + +
134A ASN* 3.8 9.2 - - + -
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Residues in contact with TYR 98 (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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31A ALA* 4.0 5.8 - - - -
97A VAL* 1.3 73.9 - - - +
99A SER* 1.3 65.5 + - - +
100A VAL* 4.1 12.1 - - + -
105A SER* 3.3 31.2 - - - +
106A PHE* 3.5 37.3 - + + -
109A SER* 3.9 4.5 - - - -
131A LEU* 3.8 31.9 - - + -
132A LEU 2.8 12.0 + - - +
133A GLY* 3.4 24.8 - - - -
134A ASN* 2.6 36.0 + - - +
144A VAL* 4.1 14.2 - - + +
145A THR 4.6 0.3 + - - -
149A GLY* 3.6 8.7 - - - -
160A PHE* 3.2 25.7 - + - -
162A GLU* 4.4 4.5 + - - -
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Residues in contact with SER 99 (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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30A GLY 5.0 0.4 - - - -
31A ALA* 4.2 6.9 - - - +
98A TYR* 1.3 80.3 - - - +
100A VAL* 1.3 58.9 + - - +
101A ASP* 2.4 29.4 + - - -
102A SER* 3.0 34.9 + - - +
105A SER* 3.1 12.0 + - - -
134A ASN 3.5 5.4 - - - -
135A LYS* 3.0 35.8 - - - +
144A VAL* 4.7 0.3 - - - +
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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