Contacts of the strand formed by residues 107 - 115 (chain B) in PDB entry 5I7L
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 ASP 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.4 7.4 - - - +
103B ASN* 6.3 0.9 - - + +
106B ILE* 1.3 74.8 - - - +
108B ILE* 1.3 78.9 + - - +
109B LYS* 4.9 9.9 + - - +
140B GLN 3.3 1.1 - - - +
141B VAL* 3.3 4.0 - - - +
142B ASN* 2.6 53.5 + - + +
144B PRO* 3.6 29.8 - - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 4.1 30.4 - - + +
74B LEU* 4.2 20.4 + - + +
77B LEU* 3.9 27.6 - - + -
106B ILE* 4.3 19.7 - - + -
107B ASP* 1.3 87.1 + - - +
109B LYS* 1.3 60.6 + - - +
110B VAL* 4.0 4.2 + - - +
139B LEU* 4.1 24.5 - - + -
140B GLN 3.0 10.3 - - - +
141B VAL* 4.3 10.5 - - + -
207B LEU* 4.7 13.9 - - + -
211B LEU* 5.6 3.6 - - + -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 4.2 11.1 + - - +
108B ILE* 1.3 74.8 - - - +
110B VAL* 1.3 64.9 + - - +
111B THR* 3.5 19.0 + - - +
138B LYS 3.8 0.2 - - - +
139B LEU* 3.8 0.3 - - - -
140B GLN* 2.9 65.4 + - + +
142B ASN* 4.5 11.4 - - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU 3.5 22.2 - - - +
69B GLU* 3.2 40.9 + - - +
71B LEU* 4.5 17.0 - - + +
73B LEU* 4.4 14.6 - - + -
108B ILE 4.0 3.6 + - - +
109B LYS* 1.3 72.7 - - - +
111B THR* 1.3 62.0 + - - +
113B PRO* 5.8 0.2 - - + -
137B ILE* 4.1 29.6 - - + -
138B LYS 3.6 3.8 - - - +
139B LEU* 3.7 17.7 - - + -
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 4.8 5.1 + - - -
109B LYS* 3.5 24.9 + - - +
110B VAL* 1.3 75.5 - - - +
112B ASP* 1.3 88.9 + - + +
113B PRO* 3.3 6.4 - - - +
137B ILE* 3.8 5.0 - - - +
138B LYS* 2.9 55.9 + - + +
139B LEU 5.3 0.2 - - - -
140B GLN* 5.1 4.0 - - + +
152B ARG* 5.7 4.3 - - + +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 4.9 1.0 + - - -
111B THR* 1.3 93.8 + - - +
113B PRO* 1.3 74.9 - - - +
114B GLN* 4.2 11.8 - - - +
136B GLY 3.8 6.2 - - - +
137B ILE* 3.9 5.0 - - - -
138B LYS* 4.1 30.6 + - + +
152B ARG* 5.5 1.4 + - - -
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.3 48.4 - - + +
68B LEU* 3.8 17.9 - - + -
69B GLU* 3.2 31.9 - - + +
111B THR 3.3 6.2 - - - +
112B ASP* 1.3 93.2 - - - +
114B GLN* 1.3 65.0 + - - +
136B GLY 3.3 8.1 - - - +
137B ILE* 4.2 3.4 - - + -
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.6 9.6 - - - +
68B LEU* 4.1 6.1 - - - +
112B ASP* 4.4 9.7 + - - +
113B PRO* 1.3 82.1 - - - +
115B LEU* 1.3 63.4 + - - +
116B LEU* 4.2 11.5 - - + +
135B LEU* 3.4 6.2 - - - +
136B GLY* 3.0 39.8 + - - +
138B LYS* 5.5 8.3 + - - +
156B LYS* 3.1 25.9 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER* 3.8 28.7 - - - +
59B LEU* 4.2 16.6 - - + -
60B LEU* 3.9 36.8 - - + +
64B LEU* 4.1 15.0 - - + -
65B LEU* 4.1 3.6 - - + +
114B GLN* 1.3 75.9 - - - +
116B LEU* 1.3 86.1 + - - +
118B LEU* 4.0 4.5 - - + -
133B ILE* 3.5 31.2 - - + -
134B PRO 3.7 5.8 - - - +
135B LEU* 4.4 1.3 - - + -
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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