Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 4YCG
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 GLN 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR 3.9 2.7 + - - -
98A ALA* 3.7 15.9 - - - +
99A ALA* 2.8 35.4 + - + +
105A PHE* 1.3 71.5 - - - +
107A LYS* 1.3 61.2 + - - +
108A HIS* 3.8 6.0 + - - +
205A VAL 3.7 0.7 - - - +
206A THR* 3.1 7.3 - - - -
207A VAL* 2.8 42.1 + - + +
216A THR* 6.1 2.2 - - - -
217A LEU 3.8 14.6 - - - +
218A ASP* 3.1 42.7 + - + +
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Residues in contact with LYS 107 (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 ILE 3.8 0.8 - - - +
96A SER* 3.4 4.3 - - - -
97A THR* 2.8 59.6 + - + +
98A ALA 3.1 18.8 + - - -
100A THR* 3.6 13.3 + - - +
103A PHE* 3.3 41.1 + - - +
105A PHE* 3.2 30.3 - - + +
106A GLN* 1.3 74.4 - - - +
108A HIS* 1.3 64.7 + - - +
159A TRP* 5.2 3.4 - - - -
160A ASP* 3.5 38.6 - - + +
161A GLN* 4.1 4.3 - - + +
204A GLU* 5.2 1.3 - - - -
205A VAL 3.8 2.5 - - - -
206A THR* 4.6 4.9 - - + +
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Residues in contact with HIS 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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94A ALA* 6.2 0.4 - - + -
95A ILE 3.5 2.7 - - - +
96A SER* 3.0 33.4 + - - +
97A THR 5.6 0.4 - - - -
106A GLN* 3.8 10.4 - - + +
107A LYS* 1.3 78.6 + - - +
109A ILE* 1.3 63.9 + - - +
110A LEU* 3.8 17.5 + - + +
203A LEU 3.8 0.5 - - - +
204A GLU* 3.2 4.2 - - - +
205A VAL* 2.6 53.6 + - + +
207A VAL* 4.3 6.3 - - + -
218A ASP* 2.5 42.2 + - - -
219A ILE* 3.7 15.8 - - + +
221A VAL* 3.6 21.8 - - + +
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Residues in contact with ILE 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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94A ALA* 3.4 5.9 - - - -
95A ILE* 2.9 53.9 + - + +
108A HIS* 1.3 72.8 - - - +
110A LEU* 1.3 64.0 + - - +
111A ILE* 3.7 11.2 + - + +
152A VAL* 5.1 4.7 - - + -
155A ASP* 5.2 13.5 - - + -
156A SER 5.9 2.0 - - - +
159A TRP 5.4 1.1 - - - +
160A ASP* 3.3 32.8 - - + +
202A LYS* 4.0 27.1 - - + +
203A LEU 3.5 8.1 - - - +
204A GLU* 4.1 21.5 - - + +
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Residues in contact with LEU 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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91A VAL* 4.4 6.3 - - + -
93A ASP 3.9 1.8 - - - -
94A ALA* 4.2 14.4 - - + -
108A HIS* 4.4 12.3 - - + +
109A ILE* 1.3 76.2 - - - +
111A ILE* 1.3 60.9 + - - +
112A PHE* 3.4 25.4 - - + -
127A LEU* 4.5 1.3 - - + -
129A LEU* 4.0 26.7 - - + -
202A LYS* 3.4 4.2 - - - -
203A LEU* 2.8 49.6 + - + +
205A VAL* 4.0 11.7 - - + -
219A ILE* 4.7 2.0 - - + -
221A VAL* 4.0 24.0 - - + -
229A PRO* 4.0 16.4 - - + -
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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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91A VAL* 3.4 2.8 - - - +
92A GLU* 2.7 40.9 + - + +
93A ASP* 2.8 41.7 + - + +
95A ILE* 4.5 19.3 - - + -
109A ILE* 4.4 8.1 - - + +
110A LEU* 1.3 72.8 - - - +
112A PHE* 1.3 65.2 + - - +
200A LYS 6.1 0.2 - - - +
201A ASN 4.5 4.3 - - - +
202A LYS* 4.0 35.9 - - + +
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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