Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 4LL4
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 TYR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL 3.6 1.6 - - - +
32A ILE* 3.4 4.9 - - - -
33A VAL 2.8 46.5 + - - +
34A GLU* 5.2 2.5 - - - -
35A VAL* 5.5 1.1 - - + -
78A LEU* 4.1 26.2 - - + -
89A VAL* 5.4 0.9 - - + -
90A ILE 3.7 8.1 + - - -
91A MET* 3.4 47.3 - - + -
92A ARG* 2.7 50.1 + - - +
95A ASN* 3.2 31.7 + - + -
96A LYS* 1.3 73.0 - - - +
98A GLU* 1.3 59.5 + - - +
99A TYR* 4.1 3.4 - - - -
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Residues in contact with GLU 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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30A ARG* 3.5 30.8 + - - -
31A VAL 3.6 2.2 - - - -
32A ILE* 3.8 21.9 - - + +
77A LEU 5.2 0.2 - - - +
78A LEU* 3.9 18.8 - - - +
79A GLU* 5.1 7.8 + - - +
96A LYS* 3.8 29.7 + - - +
97A TYR* 1.3 75.2 - - - +
99A TYR* 1.3 64.1 + - - +
100A LYS* 4.1 3.3 + - + +
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Residues in contact with TYR 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 ARG* 2.8 23.2 - - - +
31A VAL* 2.8 34.9 + - + +
33A VAL* 4.2 7.4 - - + -
41A VAL* 4.3 5.9 - - - +
43A ALA 5.3 0.2 - - - -
44A VAL* 3.3 38.5 + - + +
76A LEU* 3.7 32.7 - - + +
77A LEU* 3.7 21.1 - - - -
78A LEU* 3.5 36.2 - - + +
89A VAL* 5.0 6.6 - - - +
91A MET* 3.1 30.0 - - + +
97A TYR 4.1 5.4 - - - -
98A GLU* 1.3 77.6 - - - +
100A LYS* 1.3 60.9 - - - +
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Residues in contact with LYS 100 (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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29A GLY 3.4 10.3 - - - +
30A ARG* 4.1 8.5 - - + -
76A LEU* 3.5 20.9 - - - +
77A LEU 5.2 5.2 + - - -
79A GLU* 3.8 34.9 + - + +
98A GLU* 4.1 2.8 + - + +
99A TYR* 1.3 72.5 - - - +
101A PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 101 (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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12A VAL* 4.2 13.2 - - + -
13A VAL 4.7 0.9 - - - -
14A PHE* 3.9 26.9 - + - -
27A VAL 4.2 0.7 - - - -
28A ALA* 3.3 11.8 - - - +
29A GLY* 3.1 34.5 + - - +
30A ARG* 3.4 34.1 - - - -
31A VAL* 4.0 17.9 - - + -
46A ILE* 3.3 28.9 - - + -
74A ASP* 5.9 0.2 - - - -
76A LEU* 3.7 9.2 - - + -
100A LYS* 1.3 78.1 - - - +
102A GLY* 1.3 62.0 + - - +
103A PHE* 4.0 28.5 - + - -
125A VAL* 4.8 6.1 - - + -
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Residues in contact with GLY 102 (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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26A LYS* 4.3 18.4 + - - -
27A VAL 3.6 7.9 - - - -
28A ALA* 4.3 6.3 - - - -
72A TYR* 3.3 19.3 + - - -
101A PHE* 1.3 77.3 - - - +
103A PHE* 1.3 62.9 + - - -
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Residues in contact with PHE 103 (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 LYS* 3.5 6.1 - - - +
27A VAL* 2.7 69.6 + - + +
46A ILE* 4.7 2.5 - - + -
48A ALA* 3.5 22.0 - - + -
70A LEU* 3.7 32.5 - - + -
72A TYR* 3.6 42.6 - + + -
101A PHE* 4.0 23.1 - + - -
102A GLY* 1.3 77.9 - - - +
104A GLU* 1.3 62.4 + - - +
105A LEU* 4.7 1.6 - - + -
125A VAL* 3.9 18.8 - - + -
143A PHE* 4.2 7.4 - + - -
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Residues in contact with GLU 104 (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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24A GLY 4.1 10.5 - - - +
25A GLU 3.3 11.2 - - - +
26A LYS* 3.8 32.7 + - + +
70A LEU* 5.1 3.4 - - - +
103A PHE* 1.3 80.6 - - - +
105A LEU* 1.3 70.1 + - - +
106A PRO* 3.8 0.7 - - - +
107C GLN* 5.2 9.1 + - - +
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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