Contacts of the strand formed by residues 111 - 119 (chain G) in PDB entry 5IC4
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 ARG 111 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41G TYR* 3.9 4.4 - - - -
43G GLU* 3.1 34.2 + - + +
45G GLY* 3.6 24.7 - - - -
46G LEU* 3.4 23.3 - - - +
84G GLU* 3.7 16.6 + - - -
86G ARG* 4.3 3.6 - - - +
106G GLU* 3.0 29.9 + - - +
107G ASP 3.9 15.5 + - - +
108G HIS* 2.9 38.5 + - + +
109G SER 3.3 0.4 - - - -
110G LYS* 1.3 81.8 - - - +
112G SER* 1.3 62.6 + - - +
113G SER 4.0 5.8 - - - +
151G LEU* 5.4 0.2 - - + -
154G LYS* 3.1 27.4 + - - +
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Residues in contact with SER 112 (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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38G LYS 3.9 6.1 - - - +
39G MET* 3.3 38.1 + - - +
41G TYR* 3.2 32.5 + - - +
43G GLU 2.9 16.8 + - - -
44G MET* 3.4 11.8 + - - -
111G ARG* 1.3 73.6 - - - +
113G SER* 1.3 61.3 + - - +
154G LYS* 3.4 21.6 - - - +
155G PRO* 3.5 8.5 - - - +
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Residues in contact with SER 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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39G MET* 3.9 7.1 - - - +
44G MET 2.9 12.1 + - - -
45G GLY* 3.3 20.1 - - - -
46G LEU 4.0 0.9 + - - -
83G TYR* 2.9 28.9 + - - -
108G HIS* 5.0 1.0 + - - -
111G ARG* 3.4 7.7 + - - +
112G SER* 1.3 79.8 - - - +
114G PHE* 1.3 64.9 + - - +
115G VAL* 5.4 0.9 - - - -
151G LEU* 4.2 7.2 - - - +
154G LYS* 4.6 3.6 - - - -
155G PRO* 3.3 29.6 - - - -
157G LEU* 5.5 3.6 - - - -
273H LEU* 5.6 0.4 - - - -
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Residues in contact with PHE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU* 4.0 18.4 - - + -
48G ILE* 3.8 16.6 - - + -
100G MET* 4.0 10.1 - - + -
103G VAL* 3.6 22.4 - - + -
108G HIS* 4.2 11.7 - + - +
113G SER* 1.3 77.9 - - - +
115G VAL* 1.3 69.6 + - - +
116G CYS* 3.8 24.9 - - + -
143G PHE* 3.4 39.3 - + - -
151G LEU* 3.7 22.9 - - + -
155G PRO 3.1 7.2 + - - +
156G LYS* 3.5 8.3 - - + -
157G LEU* 2.8 27.4 + - - +
158G PHE* 4.0 15.3 - + - -
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Residues in contact with VAL 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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46G LEU 3.0 11.3 + - - +
47G CYS* 3.2 17.4 - - + -
48G ILE 2.8 25.3 + - - -
78G PHE* 4.0 28.0 - - + -
83G TYR* 3.6 27.8 - - + +
113G SER* 4.8 0.2 - - - +
114G PHE* 1.3 85.9 - - - +
116G CYS* 1.3 63.7 + - - +
117G VAL* 4.1 10.8 - - + -
157G LEU* 3.4 30.5 - - + +
159G ILE* 4.4 7.4 - - + -
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Residues in contact with CYS 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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48G ILE* 3.3 11.9 - - + -
50G ILE* 5.0 0.2 - - - -
100G MET* 3.5 25.8 - - - -
114G PHE* 3.8 13.6 - - + -
115G VAL* 1.3 75.6 - - - +
117G VAL* 1.3 63.7 + - - +
118G LEU* 3.8 29.6 + - - +
139G ILE* 5.1 0.4 - - - -
157G LEU 2.8 9.7 + - - +
158G PHE* 3.3 29.1 - - + +
159G ILE* 2.8 26.5 + - - +
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Residues in contact with VAL 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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47G CYS* 4.5 4.3 - - - -
48G ILE 2.6 13.5 + - - +
49G ILE* 4.1 18.4 - - + -
50G ILE 2.8 28.9 + - - +
74G LEU* 3.6 36.1 - - + -
78G PHE* 4.6 1.3 - - + -
115G VAL* 4.1 10.5 - - + -
116G CYS* 1.3 76.9 - - - +
118G LEU* 1.3 65.9 + - - +
119G LEU* 4.0 15.7 - - + -
159G ILE* 3.3 37.0 - - + +
216H ILE* 4.7 0.2 - - + -
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Residues in contact with LEU 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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50G ILE* 3.6 36.1 - - + -
96G ILE* 5.3 4.3 - - + -
116G CYS* 3.8 19.1 - - - +
117G VAL* 1.3 76.9 - - - +
119G LEU* 1.3 64.1 + - - +
120G SER 4.0 1.1 - - - -
127G ILE* 4.0 28.5 - - + -
136G LEU* 3.6 31.4 - - + -
139G ILE* 4.9 13.0 - - + -
158G PHE* 5.2 5.2 - - + -
159G ILE 2.8 12.9 + - - +
160G ILE* 4.3 12.4 - - + +
161G GLN 2.9 30.5 + - - +
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Residues in contact with LEU 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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49G ILE* 4.1 11.9 - - + -
50G ILE 2.9 13.8 + - - +
51G ASN* 3.8 15.9 - - + +
52G ASN 2.8 26.0 + - - -
64G ARG* 3.1 7.9 + - - +
67G THR* 3.8 14.8 - - - +
70G ASP* 4.2 6.3 - - + +
71G ALA* 4.0 19.5 - - + +
74G LEU* 3.7 19.1 - - + -
117G VAL* 4.0 10.1 - - + -
118G LEU* 1.3 74.3 - - - +
120G SER* 1.3 62.3 + - - +
161G GLN* 3.6 28.7 - - + -
216H ILE* 3.7 24.2 - - + -
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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