Contacts of the strand formed by residues 112 - 122 (chain G) in PDB entry 2YGD
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 112 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109G ASP* 2.8 40.6 + - - +
111G HIS* 1.3 78.1 - - - +
113G PHE* 1.3 68.3 + - - -
114G ILE* 5.0 0.4 - - - -
121J LYS 3.4 13.7 - - - -
122J TYR* 3.5 21.1 - - - -
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Residues in contact with PHE 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLU* 3.5 15.9 - - - +
107G ARG 4.1 2.2 - - - -
108G GLN* 3.7 40.2 - - + -
109G ASP 4.5 4.9 - - - -
110G GLU 5.4 1.6 - - - -
111G HIS* 4.3 21.1 - - - -
112G GLY* 1.3 85.7 - - - -
114G ILE* 1.3 63.0 + - - +
115G SER* 3.8 2.9 - - - +
119J HIS 3.8 5.5 - - - +
120J ARG* 6.0 0.2 - - - +
121J LYS* 3.6 45.8 + - + +
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Residues in contact with ILE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLU* 2.7 12.2 + - - -
106G GLU* 2.8 41.9 + - + +
107G ARG* 3.2 53.8 + - + +
109G ASP* 3.5 22.7 - - - +
112G GLY 5.0 0.2 - - - -
113G PHE* 1.3 76.0 - - - +
115G SER* 1.3 57.0 + - - +
80J ASP 5.5 0.7 - - - +
81J VAL* 6.1 1.8 - - - -
118J PHE* 4.9 10.3 - - + -
119J HIS 4.7 0.9 - - - -
120J ARG* 3.5 51.8 - - + +
122J TYR* 5.5 0.4 - - + +
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Residues in contact with SER 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G LYS* 4.9 13.6 - - - +
104G HIS 3.3 11.7 - - - -
105G GLU* 4.6 10.0 + - - +
113G PHE* 4.9 0.7 - - - +
114G ILE* 1.3 72.5 + - - +
116G ARG* 1.3 58.8 - - - +
117G GLU* 5.1 3.6 - - - -
118J PHE* 3.2 11.8 - - - +
119J HIS* 3.0 47.6 + - - +
120J ARG* 5.8 0.2 - - - +
121J LYS* 3.4 18.7 + - - -
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Residues in contact with ARG 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G LYS* 5.8 3.4 - - - +
83G HIS* 3.8 17.6 + - - +
84G PHE* 3.5 26.7 - - + -
103G LYS* 3.4 2.3 - - - -
104G HIS* 2.9 38.7 + - - +
106G GLU* 2.7 52.6 + - + +
114G ILE 3.6 2.6 + - - -
115G SER* 1.3 69.5 - - - +
117G GLU* 1.3 73.8 + - - +
118G PHE* 3.7 27.4 - - + -
83J HIS* 5.5 2.0 - - - -
116J ARG* 4.5 9.9 - - + +
117J GLU 3.5 5.6 - - - +
118J PHE* 3.5 26.0 - - + -
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Residues in contact with GLU 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G PHE* 4.4 0.4 - - - -
101G HIS* 2.7 32.9 + - + +
102G GLY 3.1 11.0 - - - +
103G LYS* 3.6 22.0 - - + +
115G SER* 5.1 5.2 - - - +
116G ARG* 1.3 80.8 - - - +
118G PHE* 1.3 63.3 + - - +
119G HIS* 5.9 1.6 - - + -
116J ARG* 3.4 8.5 - - - +
117J GLU* 2.7 55.2 + - + +
118J PHE* 5.3 0.9 - - - -
119J HIS* 4.5 16.8 + - - +
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Residues in contact with PHE 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASP* 4.9 4.7 - - - -
81G VAL* 3.8 38.0 - - + +
82G LYS* 3.9 37.7 - - + -
83G HIS 4.6 2.5 - - - -
84G PHE* 3.7 21.8 - + + -
100G VAL 3.8 0.3 - - - +
101G HIS* 3.5 2.6 - - - -
102G GLY 2.7 35.8 + - - +
116G ARG* 3.7 28.5 - - - -
117G GLU* 1.3 77.6 - - - +
119G HIS* 1.3 62.7 + - - +
120G ARG* 4.0 3.1 - - + +
106J GLU* 5.0 1.1 - - + -
107J ARG* 4.9 12.6 - - - -
114J ILE* 5.2 6.7 - - + -
115J SER 3.6 11.9 - - - -
116J ARG* 3.4 30.1 - - + -
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Residues in contact with HIS 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLU* 2.7 31.2 + - + -
100G VAL 3.4 16.6 - - - -
101G HIS* 4.7 15.5 - + + -
117G GLU* 5.9 2.5 - - + -
118G PHE* 1.3 74.8 - - - +
120G ARG* 1.3 60.8 + - - +
121G LYS* 3.5 26.3 + - + +
113J PHE 4.0 0.9 - - - +
115J SER* 2.8 55.1 + - - -
117J GLU* 4.6 9.3 + - + +
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Residues in contact with ARG 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G SER* 4.6 6.9 + - - -
78G ASN* 3.0 23.0 + - - +
79G LEU* 4.0 8.1 - - + +
80G ASP* 2.7 59.0 + - - +
81G VAL* 5.8 0.2 - - + -
99G GLU* 3.5 2.6 - - - +
100G VAL* 2.9 48.9 + - + +
118G PHE* 4.0 2.9 - - + +
119G HIS* 1.3 71.5 - - - +
121G LYS* 1.3 60.2 + - - +
122G TYR* 3.0 28.9 + - + -
109J ASP* 2.7 30.5 + - - -
111J HIS* 5.3 0.4 - - - -
113J PHE 3.6 10.8 - - - +
114J ILE* 3.5 30.0 - - + +
115J SER 4.3 0.6 + - - -
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Residues in contact with LYS 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLU* 3.6 24.9 - - + +
119G HIS* 3.6 24.9 - - + +
120G ARG* 1.3 73.6 - - - +
122G TYR* 1.3 66.8 + - - +
105J GLU* 4.9 6.5 + - - +
112J GLY* 3.8 1.2 - - - -
113J PHE* 3.0 70.0 + - + +
115J SER* 2.8 28.3 + - - +
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Residues in contact with TYR 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G SER* 5.1 0.9 + - - -
77G VAL* 3.2 35.2 - - + +
78G ASN 3.9 2.6 + - - -
79G LEU* 3.3 27.4 - - + -
97G VAL* 3.4 22.2 - - - +
98G ILE* 3.2 29.4 + - + +
99G GLU* 4.4 2.1 - - - +
120G ARG* 3.0 39.7 + - + -
121G LYS* 1.3 82.3 - - - +
123G ARG* 1.3 62.7 + - - +
124G ILE* 3.5 19.7 - - + -
109J ASP* 3.1 7.3 + - - -
111J HIS* 3.0 43.7 - + + +
112J GLY* 4.8 1.3 - - - -
113J PHE 5.6 1.1 - - - -
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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