Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 2FV7
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 GLY 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A CYS 4.1 3.2 + - - -
25A MET* 3.2 9.6 - - - -
26A THR 2.8 22.2 + - - -
74A LYS 5.5 0.4 + - - -
75A VAL* 5.5 0.6 - - - +
105A ALA 3.4 2.4 + - - -
106A THR* 1.4 80.1 - - - +
108A THR* 1.3 59.4 + - - +
124A VAL 3.3 4.9 - - - -
125A ALA* 3.2 25.9 + - - -
126A GLY 4.4 0.2 - - - -
127A ALA* 4.0 4.2 - - - +
128A ASN* 3.7 12.6 - - - +
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Residues in contact with THR 108 (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 MET* 4.1 4.7 - - - +
26A THR* 3.2 10.5 - - - +
28A LEU* 4.3 15.0 - - + -
80A PHE* 3.8 30.5 - - + -
105A ALA* 5.5 3.4 - - + -
106A THR 3.3 17.3 + - - +
107A GLY* 1.3 74.1 - - - +
109A ALA* 1.3 61.7 + - - +
110A SER* 4.0 4.4 + - - -
122A VAL 3.8 0.7 + - - +
123A ILE* 3.4 5.5 - - - +
124A VAL* 2.9 50.1 + - - +
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Residues in contact with ALA 109 (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 MET* 4.1 13.6 - - - -
26A THR 2.8 8.9 + - - -
27A ASP* 3.3 22.6 - - - +
28A LEU* 2.9 25.9 + - - +
108A THR* 1.3 74.2 - - - +
110A SER* 1.3 61.6 + - - +
111A ILE* 3.6 14.4 + - + +
121A ILE* 4.4 10.8 - - + -
122A VAL 3.5 4.9 - - - -
123A ILE* 4.3 4.5 - - + +
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Residues in contact with SER 110 (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 LEU* 3.8 25.3 - - - +
108A THR* 4.0 5.1 + - - -
109A ALA* 1.3 70.4 - - - +
111A ILE* 1.3 59.0 + - - +
112A ILE* 4.2 4.5 + - - +
120A ILE 3.7 1.6 - - - +
121A ILE* 3.3 4.0 - - - -
122A VAL* 2.8 48.8 + - - +
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Residues in contact with ILE 111 (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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27A ASP* 3.9 25.8 - - + -
28A LEU 3.0 11.2 + - - +
29A VAL* 3.5 16.2 - - + +
30A SER* 3.0 26.3 + - - +
109A ALA* 3.8 20.2 - - + +
110A SER* 1.3 78.1 - - - +
112A ILE* 1.3 65.5 + - - +
113A VAL* 3.6 24.2 - - + -
119A ASN* 4.6 2.7 - - + +
120A ILE 3.6 2.5 - - - -
121A ILE* 4.0 36.6 - - + -
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Residues in contact with ILE 112 (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 SER* 3.5 17.3 - - - +
32A THR* 4.0 21.5 - - + +
35A LEU* 3.7 18.9 - - + +
36A PRO* 4.3 17.9 - - + -
42A ILE* 5.2 0.4 - - + -
110A SER* 5.2 3.1 - - - +
111A ILE* 1.3 77.8 - - - +
113A VAL* 1.3 62.7 + - - +
119A ASN* 3.1 7.6 - - - +
120A ILE* 3.0 59.3 + - + +
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Residues in contact with VAL 113 (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 VAL* 4.4 5.8 - - + -
30A SER 3.0 5.7 + - - -
31A LEU* 3.5 27.2 - - + +
32A THR* 2.8 28.8 + - - +
35A LEU* 4.3 0.2 - - - -
111A ILE* 3.6 22.2 - - + -
112A ILE* 1.3 79.8 - - - +
114A ASN* 1.3 75.1 + - - +
117A GLY* 4.3 13.7 - - - +
118A GLN 3.4 8.5 - - - +
119A ASN* 4.2 7.6 - - + +
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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