Contacts of the strand formed by residues 107 - 113 (chain N) in PDB entry 3SDI
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 LYS 107 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8N PHE 4.2 8.3 - - - +
9N LYS* 3.1 32.2 + - - +
10N ASP 4.6 1.3 - - - -
11N GLY 4.5 3.4 - - - +
76N THR* 5.4 0.2 + - - -
103N GLY 3.6 1.6 - - - +
104N TYR* 3.6 27.7 - - + +
105N ASP* 2.7 44.5 + - + +
106N ASN* 1.3 78.9 - - - +
108N GLY* 1.3 67.2 + - - +
109N GLU* 3.9 1.4 + - - +
145N ASN* 4.4 14.5 - - - +
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Residues in contact with GLY 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N THR* 3.6 17.0 - - - +
11N GLY* 3.6 27.5 + - - -
12N VAL* 4.2 1.6 - - - -
103N GLY 3.6 6.3 - - - -
104N TYR* 3.9 2.9 - - - -
106N ASN 3.9 2.3 - - - +
107N LYS* 1.3 87.3 - - - +
109N GLU* 1.3 65.1 + - - +
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Residues in contact with GLU 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N THR* 4.1 2.7 - - - +
12N VAL* 4.2 2.0 - - - +
76N THR* 3.9 17.7 + - - +
77N GLU* 4.1 3.8 + - - +
101N VAL 4.1 0.6 - - - +
102N ALA* 3.5 2.1 - - - +
103N GLY 3.1 32.4 + - - +
106N ASN* 3.5 41.8 + - + +
107N LYS 4.6 1.6 - - - +
108N GLY* 1.3 78.6 - - - +
110N VAL* 1.3 69.8 + - - +
111N TYR* 2.8 37.1 + - + -
121N LYS* 3.5 25.4 + - - +
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Residues in contact with VAL 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N ALA* 3.6 25.1 - - + +
7N THR* 4.0 9.4 - - + +
12N VAL* 3.5 25.1 - - + -
100N ILE* 4.1 13.9 - - + -
101N VAL 3.6 2.5 - - - -
102N ALA* 4.2 2.5 - - + -
109N GLU* 1.3 80.0 - - - +
111N TYR* 1.3 68.3 + - - +
121N LYS* 3.4 8.5 - - - +
122N LEU* 2.9 47.1 + - + +
123N PRO 4.7 1.1 - - - +
124N TYR 4.4 0.2 - - - -
125N ALA* 3.9 28.7 - - + +
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Residues in contact with TYR 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N THR* 4.0 16.2 - - + -
77N GLU* 3.4 44.5 + - + +
80N ALA* 3.7 28.0 - - + -
99N ILE 4.2 0.2 - - - +
100N ILE* 3.5 4.3 - - - +
101N VAL* 2.7 45.4 + - + +
109N GLU* 2.8 34.8 + - + -
110N VAL* 1.3 77.0 - - - +
112N THR* 1.3 59.6 + - - +
113N ILE* 5.1 0.4 - - + -
119N VAL* 4.2 15.9 - - + -
120N HIS 3.2 6.5 - - - +
121N LYS* 3.6 43.7 - - + +
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Residues in contact with THR 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M ARG* 4.7 10.8 + - - +
27M PHE* 3.9 22.7 - - + -
99N ILE 3.6 3.8 + - - -
100N ILE* 3.6 17.0 - - - +
110N VAL* 4.9 0.4 - - - +
111N TYR* 1.3 75.8 - - - +
113N ILE* 1.3 65.7 + - - +
114N PRO* 3.6 4.7 - - + +
119N VAL* 3.5 3.7 - - - -
120N HIS* 2.8 38.2 + - + +
122N LEU* 3.8 25.8 - - + +
125N ALA* 4.1 16.6 - - + +
126N ILE 5.3 0.9 + - - -
127N ALA* 5.1 2.4 - - - +
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Residues in contact with ILE 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N ALA* 3.8 12.1 - - + +
83N PHE* 3.7 28.9 - - + -
84N LYS* 4.6 7.0 - - - +
87N CYS* 4.0 27.6 - - + -
97N ALA 4.3 0.4 - - - +
98N GLY* 3.5 1.0 - - - -
99N ILE* 2.8 39.3 + - + +
101N VAL* 3.7 22.4 - - + -
111N TYR 5.1 0.7 - - - +
112N THR* 1.3 78.1 + - - +
114N PRO* 1.3 69.9 - - - +
117N GLY* 4.1 10.5 - - - -
118N SER 3.2 13.5 - - - +
119N VAL* 3.8 16.8 - - + -
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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