Contacts of the strand formed by residues 101 - 108 (chain B) in PDB entry 4DAY
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 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.1 37.1 + - + +
62B GLY* 3.7 20.8 + - - -
63B ARG* 3.7 33.7 - - + +
75B ARG 5.1 1.1 - - - -
76B ASP* 5.5 1.7 - - - +
77B PRO* 5.7 1.8 - - + +
100B LYS* 1.3 73.0 - - - +
102B VAL* 1.3 61.1 + - - +
124B ASP* 2.9 18.2 - - - +
125B LEU* 2.9 32.4 + - + +
126B SER* 3.0 17.0 + - - +
128B ASN 5.6 0.9 - - - -
131B HIS* 4.0 4.5 - - + -
132B GLU* 3.5 43.3 + - + -
135B TRP* 3.2 23.7 - - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B MET 4.1 0.3 - - - +
61B GLN* 3.3 3.9 - - - +
62B GLY 3.2 27.3 + - - -
64B VAL* 4.4 4.3 - - + -
74B LEU* 3.7 32.7 - - + +
96B LEU* 4.5 20.6 - - + -
100B LYS* 4.6 2.0 - - + -
101B TYR* 1.3 83.0 - - - +
103B MET* 1.3 59.0 + - - +
104B VAL* 4.5 1.8 - - + -
122B MET* 4.3 24.5 - - + -
123B THR 3.3 13.7 - - - +
124B ASP* 3.4 20.4 - - + +
125B LEU* 4.0 7.2 - - - +
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 3.7 31.9 - - + -
589A CYS* 5.1 6.1 - - - -
59B TRP* 3.5 41.5 - - + +
60B MET 3.4 3.8 - - - +
61B GLN* 3.5 23.6 - - + +
102B VAL* 1.3 73.1 - - - +
104B VAL* 1.3 73.2 + - - +
105B MET* 3.8 3.6 - - + +
121B LYS 4.6 1.3 - - - +
122B MET* 3.2 4.7 - - - +
123B THR* 2.8 71.1 + - + +
125B LEU* 3.7 13.9 - - + +
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Residues in contact with VAL 104 (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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58B VAL 3.6 1.0 - - - +
59B TRP* 3.4 4.3 - - - -
60B MET* 2.7 38.9 + - - +
74B LEU* 4.1 24.5 - - + -
81B PHE* 5.2 0.2 - - + -
83B VAL* 4.2 16.4 - - + -
86B LEU* 5.3 2.2 - - + -
102B VAL* 4.5 2.7 - - + -
103B MET* 1.3 80.6 - - - +
105B MET* 1.3 74.0 + - - +
106B GLY* 3.8 5.5 + - - +
117B LEU* 4.1 21.2 - - + +
119B ALA* 4.6 9.9 - - + -
121B LYS 3.6 3.6 - - - +
122B MET* 3.6 21.3 - - + -
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 3.9 33.7 - - + -
515A VAL* 4.4 13.7 - - - -
540A TYR* 3.6 26.5 - - + +
17B LEU* 4.9 2.9 - - + -
18B PRO* 4.0 24.5 - - + -
22B PRO* 3.8 20.0 - - + -
57B ALA* 4.9 5.4 - - + -
58B VAL 3.2 13.9 - - - +
59B TRP* 4.7 0.7 - - - +
103B MET* 3.8 3.3 - - + -
104B VAL* 1.3 76.6 - - - +
106B GLY* 1.3 58.8 + - - +
120B VAL* 2.8 44.2 + - + -
121B LYS* 2.6 23.6 + - + +
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Residues in contact with GLY 106 (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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57B ALA* 3.6 3.0 - - - +
58B VAL* 2.8 36.2 + - - +
104B VAL* 3.8 5.9 + - - +
105B MET* 1.3 76.4 - - - +
107B VAL* 1.3 64.7 + - - -
117B LEU* 3.5 15.4 - - - +
118B GLN 3.3 13.0 - - - -
119B ALA* 4.2 1.3 - - - -
120B VAL* 4.0 4.0 - - - -
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Residues in contact with VAL 107 (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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18B PRO* 5.0 2.9 - - + -
56B ALA* 3.4 17.3 - - + +
57B ALA* 4.5 10.1 - - + +
106B GLY* 1.3 76.2 - - - +
108B VAL* 1.3 74.0 + - - +
109B GLN* 5.0 2.9 - - - +
117B LEU* 3.4 1.7 - - - +
118B GLN* 2.7 48.9 + - + +
120B VAL* 3.8 22.2 - - + -
1236C PHE* 3.9 26.2 - - + -
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Residues in contact with VAL 108 (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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30B LEU* 3.8 34.5 - - + -
56B ALA* 3.0 23.7 + - - +
58B VAL* 3.8 26.0 - - + -
107B VAL* 1.3 80.0 - - - +
109B GLN* 1.3 73.7 + - - +
110B ALA 4.5 0.4 - - - +
111B CYS* 4.0 19.5 - - - +
115B PRO* 5.9 1.1 - - + -
116B CYS 3.8 9.6 - - - +
117B LEU* 3.7 3.8 - - + +
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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