Contacts of the strand formed by residues 115 - 121 (chain A) in PDB entry 3CY2
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 SER 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A HIS* 5.1 7.2 + - - -
69A VAL 3.2 19.3 - - - -
70A GLU* 4.2 5.6 - - - -
71A LYS* 3.6 9.4 - - - +
111A GLU* 3.7 0.9 - - - -
112A ARG* 2.7 58.7 + - - +
113A PRO 3.6 0.2 - - - -
114A ASP* 1.3 83.1 + - - +
116A PHE* 1.3 67.4 + - - +
117A VAL* 4.6 1.7 - - - +
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Residues in contact with PHE 116 (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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67A LYS 3.5 0.9 - - - +
68A HIS* 3.5 2.9 - - - -
69A VAL* 2.9 36.9 + - + +
71A LYS* 3.7 15.0 - - - -
74A ILE* 3.8 8.5 - - + -
77A TRP* 3.5 26.9 - + - -
85A ARG 3.8 18.2 - - - -
87A PRO* 3.5 33.0 - - + -
90A VAL* 5.3 0.9 - - + -
109A TRP* 3.7 24.7 - + - -
110A PHE 3.4 13.0 - - - -
111A GLU* 3.6 33.7 - - + -
115A SER* 1.3 77.4 - - - +
117A VAL* 1.3 62.6 + - - +
118A LEU* 4.0 15.9 - - + -
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Residues in contact with VAL 117 (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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34A LEU* 3.3 37.9 - - + -
66A ILE* 3.4 31.4 - - + -
67A LYS 3.3 4.5 - - - +
68A HIS* 3.8 19.5 - - + +
109A TRP* 3.1 6.4 - - - +
110A PHE* 2.9 39.3 + - + +
112A ARG* 3.6 27.6 - - + +
115A SER* 4.6 1.6 - - - +
116A PHE* 1.3 76.4 - - - +
118A LEU* 1.3 62.4 + - - +
119A ILE* 4.1 4.0 - - + -
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Residues in contact with LEU 118 (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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65A ALA 3.4 3.6 - - - +
66A ILE* 3.5 1.7 - - - -
67A LYS* 2.7 58.5 + - + +
69A VAL* 4.7 7.0 - - + -
87A PRO* 5.5 1.1 - - + -
89A GLU* 3.8 26.7 - - + +
90A VAL* 3.8 26.0 - - + -
93A LEU* 3.8 26.2 - - + -
106A LEU* 4.0 14.4 - - + -
108A ASP 3.9 2.7 - - - -
109A TRP* 4.3 3.6 - - + -
116A PHE* 4.0 20.2 - - + +
117A VAL* 1.3 81.4 - - - +
119A ILE* 1.3 61.8 + - - +
120A LEU* 3.9 5.7 + - + +
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Residues in contact with ILE 119 (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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34A LEU* 4.9 1.6 - - + -
38A TYR* 3.6 57.0 - - + +
64A VAL* 3.8 22.7 - - + -
65A ALA 3.5 1.6 - - - -
66A ILE* 4.1 25.8 - - + -
106A LEU* 3.3 7.2 - - - +
107A LEU* 2.7 39.5 + - + -
108A ASP 2.9 25.0 + - - +
110A PHE* 3.8 22.0 - - + -
117A VAL* 4.5 2.7 - - + -
118A LEU* 1.3 74.6 - - - +
120A LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 120 (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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64A VAL* 3.2 8.1 - - - +
65A ALA* 2.8 40.8 + - + +
67A LYS* 4.3 22.4 - - + -
93A LEU* 4.2 15.9 - - + -
104A ILE* 4.0 25.8 - - + -
105A ARG 3.5 3.4 - - - +
106A LEU* 4.0 29.6 - - + -
107A LEU* 4.0 4.5 - - - -
118A LEU* 4.5 6.5 - - + +
119A ILE* 1.3 73.7 - - - +
121A GLU* 1.3 62.9 + - - +
401A CL 3.8 25.6 - - + -
501A MB9 4.3 13.9 - - + -
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Residues in contact with GLU 121 (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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62A LEU* 4.1 23.3 - - + +
63A PRO 4.2 2.2 - - - +
104A ILE* 3.1 27.5 - - + +
105A ARG* 2.5 63.3 + - + +
107A LEU* 3.5 32.2 - - + +
120A LEU* 1.3 74.1 - - - +
122A ARG* 1.3 60.7 + - - +
123A PRO* 3.9 2.0 - - - +
183A LYS* 5.6 7.1 + - - -
501A MB9 4.3 2.1 - - - +
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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