Contacts of the strand formed by residues 43 - 51 (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 GLU 43 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G MET 6.0 0.2 - - - -
41G TYR* 3.6 4.4 - - - +
42G PRO* 1.3 82.6 - - + +
44G MET* 1.3 61.2 + - - +
45G GLY* 3.3 3.7 + - - +
82G LYS 5.6 0.4 - - - -
84G GLU* 3.8 16.8 - - - +
110G LYS* 2.8 28.1 + - - +
111G ARG* 3.1 39.6 + - + +
112G SER* 2.9 28.9 + - - -
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Residues in contact with MET 44 (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* 3.7 39.9 - - + +
43G GLU* 1.3 73.7 - - - +
45G GLY* 1.3 56.9 + - - +
81G LEU 3.5 24.5 - - - +
82G LYS* 3.3 30.9 + - + +
83G TYR* 3.6 14.4 - - + -
112G SER* 3.4 4.3 + - - -
113G SER* 2.9 34.5 + - - -
275H PHE* 3.6 46.4 - - + +
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Residues in contact with GLY 45 (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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43G GLU* 3.3 6.6 - - - +
44G MET* 1.3 81.1 - - - +
46G LEU* 1.3 66.5 + - - -
83G TYR* 3.4 6.6 - - - -
84G GLU* 3.0 25.1 + - - +
111G ARG* 3.6 19.1 - - - -
113G SER 3.3 13.5 - - - -
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Residues in contact with LEU 46 (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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45G GLY* 1.3 75.2 - - - -
47G CYS* 1.3 59.9 + - - +
48G ILE* 4.5 6.3 - - + -
83G TYR* 3.6 6.2 - - - -
84G GLU* 3.3 40.8 - - + +
86G ARG* 3.5 21.8 - - - +
103G VAL* 3.9 16.4 - - + -
106G GLU* 3.3 22.9 - - - +
108G HIS* 3.7 15.5 + - + -
111G ARG* 3.4 24.3 - - - +
113G SER 4.0 4.2 + - - -
114G PHE* 4.0 13.7 - - + +
115G VAL 3.0 24.9 + - - -
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Residues in contact with CYS 47 (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* 1.3 73.4 - - - +
48G ILE* 1.3 61.9 + - - +
49G ILE* 3.6 22.5 + - - -
78G PHE* 3.8 32.5 - - - -
83G TYR* 4.0 22.9 - - + -
84G GLU 3.0 8.9 + - - -
85G VAL* 3.4 10.9 - - + +
86G ARG 2.8 26.9 + - - -
115G VAL* 3.2 18.6 - - + +
117G VAL* 4.5 2.7 - - - -
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Residues in contact with ILE 48 (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* 4.5 8.5 - - + -
47G CYS* 1.3 72.7 - - - +
49G ILE* 1.3 58.5 + - - +
50G ILE* 4.2 11.2 - - + -
86G ARG* 3.8 40.2 - - + +
88G LYS* 4.9 4.9 - - + +
99G LEU* 4.0 26.5 - - + -
100G MET* 4.4 9.9 - - - -
103G VAL* 4.2 19.7 - - + -
114G PHE* 3.8 26.0 - - + -
115G VAL 2.8 12.0 + - - +
116G CYS* 3.3 9.0 - - - -
117G VAL 2.6 33.8 + - - +
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Residues in contact with ILE 49 (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* 3.9 19.5 - - - +
48G ILE* 1.3 75.4 - - - +
50G ILE* 1.3 61.1 + - - +
51G ASN* 4.6 1.3 - - + +
71G ALA* 4.5 5.4 - - + -
74G LEU* 3.7 28.5 - - + -
75G ARG 3.9 6.5 - - - +
85G VAL* 3.7 24.7 - - + -
86G ARG 3.0 9.5 + - - +
87G ASN* 3.9 23.8 - - - +
88G LYS* 2.7 35.2 + - - +
117G VAL* 3.5 15.7 - - + -
119G LEU* 4.1 25.4 - - + -
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Residues in contact with ILE 50 (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* 4.2 12.6 - - + -
49G ILE* 1.3 74.3 - - - +
51G ASN* 1.3 59.4 + - - +
52G ASN* 3.8 22.2 - - - +
88G LYS* 3.5 5.2 - - + +
91G LEU* 4.3 15.3 - - + -
96G ILE* 3.8 33.2 - - + -
99G LEU* 4.0 22.7 - - + -
100G MET* 4.3 11.0 - - - -
116G CYS* 5.0 0.2 - - - -
117G VAL 2.8 9.7 + - - +
118G LEU* 3.6 28.5 - - + -
119G LEU* 2.9 32.1 + - - +
120G SER* 6.4 0.4 - - - -
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Residues in contact with ASN 51 (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* 4.8 2.9 - - + -
50G ILE* 1.3 70.7 - - - +
52G ASN* 1.3 62.2 + - - +
53G LYS* 3.7 3.9 + - - +
67G THR* 2.5 38.6 + - - +
68G ASP* 2.9 27.9 + - - -
71G ALA* 3.6 27.2 - - + +
87G ASN* 5.7 1.1 - - + +
88G LYS 2.6 16.0 + - - +
89G ASN* 3.3 21.8 + - - +
90G ASP* 3.0 19.6 + - - +
119G LEU* 3.8 9.0 - - + +
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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