Contacts of the strand formed by residues 31 - 35 (chain N) in PDB entry 5GAG
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 PHE 31 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26N VAL* 4.0 8.2 - - - +
30N SER* 1.3 99.4 + - - +
32N GLY* 1.3 58.9 + - - +
104N GLU* 3.3 6.8 - - - +
105N MET* 3.0 40.7 + - + +
106N ASP* 5.2 1.8 - - - -
108N VAL* 3.4 24.2 - - + -
109N PRO* 4.0 6.5 - - + -
110N GLU* 3.8 34.1 - - + -
113N ALA* 3.8 13.5 - - + -
117N PHE* 4.1 8.5 - - + -
130N PHE* 3.6 29.8 - + + -
131N VAL 3.7 3.1 - - - -
132N THR* 3.8 21.3 - - + -
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Residues in contact with GLY 32 (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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26N VAL* 4.8 1.8 - - - -
31N PHE* 1.3 78.2 - - - +
33N LEU* 1.3 60.0 + - - -
101N VAL* 4.7 5.2 - - - -
103N TYR 3.2 10.3 - - - -
104N GLU* 4.5 0.7 - - - -
117N PHE* 3.7 7.0 - - - -
130N PHE* 3.5 10.9 - - - -
131N VAL* 2.9 47.8 + - - +
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Residues in contact with LEU 33 (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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32N GLY* 1.3 71.2 - - - -
34N LYS* 1.3 58.8 + - - +
101N VAL* 3.8 3.2 - - - +
102N LEU* 3.2 31.3 + - + +
103N TYR* 2.9 44.8 + - + -
117N PHE* 3.9 38.3 - - + +
120N ALA* 5.2 2.2 - - + -
121N ALA* 4.7 4.9 - - + +
124N LEU* 4.1 20.2 - - + -
128N THR* 3.6 29.4 - - + +
129N THR 3.1 19.7 - - - +
130N PHE* 5.2 0.4 - - - -
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Residues in contact with LYS 34 (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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24N THR* 2.6 32.5 + - - -
25N ASP* 4.9 0.8 + - - -
32N GLY 3.9 0.8 + - - -
33N LEU* 1.3 74.1 - - - +
35N ALA* 1.3 68.6 + - - +
36N VAL 3.5 0.2 + - - -
99N GLY* 3.4 17.7 - - - +
100N LYS 3.3 8.1 - - - +
101N VAL* 3.8 8.1 - - + +
128N THR* 3.3 6.9 - - - -
129N THR* 2.9 44.6 + - + -
131N VAL* 3.5 35.3 - - + +
80W HIS 5.5 0.2 + - - -
81W PRO 3.3 25.4 + - - +
82W TYR* 4.0 14.3 - - + +
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Residues in contact with ALA 35 (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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33N LEU 4.1 0.6 + - - -
34N LYS* 1.3 72.5 - - - +
36N VAL* 1.3 57.6 + - - +
37N GLY 3.6 2.9 - - - +
96N ILE* 3.6 31.4 - - + -
98N PRO* 3.2 4.2 - - - +
99N GLY 2.7 32.2 + - - -
100N LYS 2.8 13.3 + - - +
102N LEU* 3.7 15.3 - - + -
126N ILE* 3.9 14.8 - - + -
128N THR* 3.9 8.1 - - + -
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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