Contacts of the strand formed by residues 103 - 112 (chain B) in PDB entry 1F15
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 LEU 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.6 16.0 - - + +
101B LYS 3.5 4.4 + - - +
102B LYS* 1.3 70.5 - - - +
104B VAL* 1.3 60.9 + - - +
174B ARG* 3.9 51.8 - - + +
175B ALA 3.2 16.8 - - - +
176B ASP* 4.6 5.6 - - + +
207B HIS* 2.9 5.5 - - - +
208B GLN* 2.6 63.5 + - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 4.6 0.2 - - - -
103B LEU* 1.3 75.4 - - - +
105B SER* 1.3 62.8 + - - +
106B ARG 4.0 4.5 - - - +
107B LEU* 3.7 21.5 - - + -
170B LEU* 4.0 11.7 - - + +
171B SER* 4.5 5.5 - - - +
174B ARG* 5.5 0.2 - - - -
175B ALA 2.7 27.8 + - - +
176B ASP 3.7 2.0 - - - -
177B ILE* 3.7 21.1 - - + +
180B MET* 3.1 38.8 - - + -
205B ILE* 4.0 12.1 - - + -
206B GLU 3.4 12.3 - - - +
207B HIS* 4.0 4.0 - - + +
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Residues in contact with SER 105 (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 ARG* 4.4 12.1 - - - -
68B TYR* 3.3 22.5 - - - -
103B LEU 3.9 1.2 + - - -
104B VAL* 1.3 74.4 - - - +
106B ARG* 1.3 67.0 + - - +
169B ASP* 3.7 0.3 - - - +
170B LEU* 3.0 6.6 + - - -
171B SER* 3.0 39.6 + - - +
206B GLU* 2.5 44.0 + - - +
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Residues in contact with ARG 106 (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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216A LEU* 4.2 9.6 - - - +
62B GLU* 4.1 17.0 + - - +
63B ARG 3.6 17.0 + - - -
65B ARG* 3.3 38.4 - - - +
104B VAL 3.8 0.2 - - - -
105B SER* 1.3 87.8 + - - +
107B LEU* 1.3 67.1 - - - +
167B LEU* 3.3 37.1 - - + +
168B TYR 3.0 21.3 - - - +
169B ASP* 3.4 21.9 + - + +
170B LEU 4.2 1.3 - - - +
204B ASP 4.0 0.9 - - - +
205B ILE 3.9 0.2 - - - -
206B GLU* 2.9 69.0 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.6 28.5 - - + -
104B VAL* 3.7 20.0 - - + -
106B ARG* 1.3 78.6 - - - +
108B GLN* 1.3 61.3 + - - +
109B ILE* 5.4 1.1 - - - -
125B VAL* 4.0 22.0 - - + +
166B LEU* 4.2 0.9 - - - +
167B LEU* 4.6 1.3 - - - -
168B TYR* 2.9 41.8 + - + +
170B LEU* 3.5 27.4 - - + -
180B MET* 3.7 15.7 - - + -
183B TYR* 4.2 12.3 - - + -
203B VAL* 4.8 5.6 - - + -
204B ASP 3.7 6.5 - - - +
205B ILE* 4.4 10.5 - - + +
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Residues in contact with GLN 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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216A LEU* 4.2 7.5 - - + +
217A PRO* 3.2 21.4 + - - +
61B SER* 2.7 24.9 + - - -
106B ARG 4.2 0.2 - - - -
107B LEU* 1.3 73.8 - - - +
109B ILE* 1.3 73.0 + - - +
110B ARG* 3.3 13.9 - - - +
165B LYS* 3.2 15.9 - - + +
166B LEU 3.3 12.1 - - - +
167B LEU* 3.5 24.3 - - + +
202B HIS 3.7 0.5 - - - +
203B VAL* 3.5 4.3 - - - +
204B ASP* 2.7 62.3 + - - +
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Residues in contact with ILE 109 (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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107B LEU 5.4 0.9 - - - -
108B GLN* 1.3 81.1 - - - +
110B ARG* 1.3 68.5 + - - +
111B VAL* 4.3 3.8 - - + -
123B VAL* 3.9 24.0 - - + -
124B THR 5.0 0.4 - - - -
125B VAL* 3.5 45.5 - - + -
151B LEU* 5.8 1.6 - - + +
165B LYS* 3.1 6.2 - - - +
166B LEU* 3.0 44.9 + - + -
185B VAL* 3.6 20.6 - - + -
201B LEU* 4.9 9.4 - - + -
202B HIS 3.5 5.8 - - - +
203B VAL* 4.1 14.4 - - + -
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Residues in contact with ARG 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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217A PRO* 3.1 25.9 - - - +
218A VAL* 3.4 28.5 + - - -
72B SER* 4.1 5.9 + - - -
108B GLN* 3.3 23.8 - - + +
109B ILE* 1.3 76.7 - - - +
111B VAL* 1.3 64.1 + - - +
112B ASN* 3.5 18.9 + - - +
164B ASN* 3.5 7.0 - - - +
165B LYS* 3.9 10.8 - - + +
200B VAL 3.7 1.6 - - - +
201B LEU* 3.2 6.8 - - - -
202B HIS* 3.0 71.0 + - + +
204B ASP* 2.9 34.3 + - - +
145C ASP 5.0 2.6 + - - -
146C GLY* 5.3 3.4 + - - -
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Residues in contact with VAL 111 (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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109B ILE* 4.9 2.7 - - + -
110B ARG* 1.3 75.0 - - - +
112B ASN* 1.3 58.4 - - - +
113B PRO* 4.1 0.7 - - - +
121B VAL* 4.9 0.2 - - + -
123B VAL* 4.3 18.4 - - + -
151B LEU* 3.8 20.9 - - + -
153B TYR* 3.9 33.0 - - + -
164B ASN* 2.8 37.9 + - - +
199B LEU* 3.4 35.2 - - + -
200B VAL 4.4 1.6 - - - -
201B LEU* 3.8 18.4 - - + -
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Residues in contact with ASN 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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218A VAL* 4.7 5.4 + - - +
58B PHE* 3.8 15.9 - - + -
110B ARG* 3.5 25.3 - - - +
111B VAL* 1.3 73.1 - - - +
113B PRO* 1.3 67.3 - - + +
164B ASN* 3.6 15.6 + - - -
199B LEU* 3.2 2.4 - - - -
200B VAL* 3.2 33.8 + - - +
202B HIS* 3.4 25.9 + - - -
143C PHE 4.8 4.6 - - - +
144C ALA* 3.7 26.9 + - + +
146C GLY* 5.0 7.2 - - - -
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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